Dec 15 21:13:38.804 INFO testing bio-0.24.0 against try#aa49d8ef14939ddec0e34b346b60174a5673d48f for pr-56550 Dec 15 21:13:38.805 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56550/worker-3/try#aa49d8ef14939ddec0e34b346b60174a5673d48f:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-3/pr-56550/try#aa49d8ef14939ddec0e34b346b60174a5673d48f:/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 +aa49d8ef14939ddec0e34b346b60174a5673d48f-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 15 21:13:39.191 INFO [stdout] aec9eb9182004f732d4cc48eb0f6dd6d07e519a7b3d01c115389d0f320ce348e Dec 15 21:13:39.203 INFO running `"docker" "start" "-a" "aec9eb9182004f732d4cc48eb0f6dd6d07e519a7b3d01c115389d0f320ce348e"` Dec 15 21:13:40.404 INFO [stderr] usermod: no changes Dec 15 21:13:40.639 INFO [stderr] Compiling bio v0.24.0 (/source) Dec 15 21:13:40.639 INFO [stderr] Compiling bv v0.10.0 Dec 15 21:13:40.639 INFO [stderr] Compiling bio-types v0.4.0 Dec 15 21:13:54.591 INFO [stderr] warning: unused import: `std::ops::Deref` Dec 15 21:13:54.591 INFO [stderr] --> src/data_structures/bwt.rs:15:5 Dec 15 21:13:54.591 INFO [stderr] | Dec 15 21:13:54.591 INFO [stderr] 15 | use std::ops::Deref; Dec 15 21:13:54.591 INFO [stderr] | ^^^^^^^^^^^^^^^ Dec 15 21:13:54.591 INFO [stderr] | Dec 15 21:13:54.591 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 15 21:13:54.591 INFO [stderr] Dec 15 21:13:56.727 INFO [stderr] warning: use of deprecated item 'ndarray::impl_methods::>::subview': renamed to `index_axis` Dec 15 21:13:56.727 INFO [stderr] --> src/stats/hmm.rs:266:22 Dec 15 21:13:56.727 INFO [stderr] | Dec 15 21:13:56.727 INFO [stderr] 266 | .subview(Axis(0), i - 1) Dec 15 21:13:56.727 INFO [stderr] | ^^^^^^^ Dec 15 21:13:56.727 INFO [stderr] | Dec 15 21:13:56.727 INFO [stderr] = note: #[warn(deprecated)] on by default Dec 15 21:13:56.727 INFO [stderr] Dec 15 21:14:02.084 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 21.64s Dec 15 21:14:02.088 INFO [stderr] su: No module specific data is present Dec 15 21:14:02.549 INFO running `"docker" "inspect" "aec9eb9182004f732d4cc48eb0f6dd6d07e519a7b3d01c115389d0f320ce348e"` Dec 15 21:14:02.761 INFO running `"docker" "rm" "-f" "aec9eb9182004f732d4cc48eb0f6dd6d07e519a7b3d01c115389d0f320ce348e"` Dec 15 21:14:03.051 INFO [stdout] aec9eb9182004f732d4cc48eb0f6dd6d07e519a7b3d01c115389d0f320ce348e Dec 15 21:14:03.059 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56550/worker-3/try#aa49d8ef14939ddec0e34b346b60174a5673d48f:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-3/pr-56550/try#aa49d8ef14939ddec0e34b346b60174a5673d48f:/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 +aa49d8ef14939ddec0e34b346b60174a5673d48f-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 15 21:14:03.468 INFO [stdout] 3e0fde7b64fd7cf135f39c050834e19598a168a709e1448ffd52a20cac6be4ca Dec 15 21:14:03.475 INFO running `"docker" "start" "-a" "3e0fde7b64fd7cf135f39c050834e19598a168a709e1448ffd52a20cac6be4ca"` Dec 15 21:14:05.021 INFO [stderr] usermod: no changes Dec 15 21:14:05.239 INFO [stderr] Compiling bio v0.24.0 (/source) Dec 15 21:14:09.451 INFO [stderr] warning: unused import: `std::ops::Deref` Dec 15 21:14:09.451 INFO [stderr] --> src/data_structures/bwt.rs:15:5 Dec 15 21:14:09.451 INFO [stderr] | Dec 15 21:14:09.451 INFO [stderr] 15 | use std::ops::Deref; Dec 15 21:14:09.451 INFO [stderr] | ^^^^^^^^^^^^^^^ Dec 15 21:14:09.451 INFO [stderr] | Dec 15 21:14:09.451 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 15 21:14:09.451 INFO [stderr] Dec 15 21:14:13.027 INFO [stderr] warning: use of deprecated item 'ndarray::impl_methods::>::subview': renamed to `index_axis` Dec 15 21:14:13.027 INFO [stderr] --> src/stats/hmm.rs:266:22 Dec 15 21:14:13.027 INFO [stderr] | Dec 15 21:14:13.027 INFO [stderr] 266 | .subview(Axis(0), i - 1) Dec 15 21:14:13.027 INFO [stderr] | ^^^^^^^ Dec 15 21:14:13.027 INFO [stderr] | Dec 15 21:14:13.027 INFO [stderr] = note: #[warn(deprecated)] on by default Dec 15 21:14:13.027 INFO [stderr] Dec 15 21:14:32.606 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 27.56s Dec 15 21:14:32.614 INFO [stderr] su: No module specific data is present Dec 15 21:14:33.327 INFO running `"docker" "inspect" "3e0fde7b64fd7cf135f39c050834e19598a168a709e1448ffd52a20cac6be4ca"` Dec 15 21:14:33.600 INFO running `"docker" "rm" "-f" "3e0fde7b64fd7cf135f39c050834e19598a168a709e1448ffd52a20cac6be4ca"` Dec 15 21:14:33.873 INFO [stdout] 3e0fde7b64fd7cf135f39c050834e19598a168a709e1448ffd52a20cac6be4ca Dec 15 21:14:33.879 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56550/worker-3/try#aa49d8ef14939ddec0e34b346b60174a5673d48f:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-3/pr-56550/try#aa49d8ef14939ddec0e34b346b60174a5673d48f:/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 +aa49d8ef14939ddec0e34b346b60174a5673d48f-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 15 21:14:34.383 INFO [stdout] 02ef8da122e30b9e40238a3467f45e4a325340e6ae43cad2db8c9ae718cf44ac Dec 15 21:14:34.384 INFO running `"docker" "start" "-a" "02ef8da122e30b9e40238a3467f45e4a325340e6ae43cad2db8c9ae718cf44ac"` Dec 15 21:14:35.951 INFO [stderr] usermod: no changes Dec 15 21:14:36.095 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 0.11s Dec 15 21:14:36.101 INFO [stdout] Dec 15 21:14:36.101 INFO [stdout] running 245 tests Dec 15 21:14:36.101 INFO [stderr] Running /target/debug/deps/bio-ff3a947848045a9f Dec 15 21:14:36.107 INFO [stdout] test alignment::pairwise::banded::banded::test_band_add_kmer ... ok Dec 15 21:14:36.107 INFO [stdout] test alignment::pairwise::banded::banded::test_band_add_entry ... ok Dec 15 21:14:36.107 INFO [stdout] test alignment::pairwise::banded::banded::test_aligner_new ... ok Dec 15 21:14:36.110 INFO [stdout] test alignment::distance::tests::test_hamming_dist_good ... ok Dec 15 21:14:36.110 INFO [stdout] test alignment::distance::tests::test_levenshtein_dist ... ok Dec 15 21:14:36.159 INFO [stdout] test alignment::pairwise::banded::banded::test_global ... ok Dec 15 21:14:36.163 INFO [stdout] test alignment::pairwise::banded::banded::test_global_affine_ins ... ok Dec 15 21:14:36.163 INFO [stdout] test alignment::pairwise::banded::banded::test_blosum62 ... ok Dec 15 21:14:36.167 INFO [stdout] test alignment::pairwise::banded::banded::test_global_right_del ... ok Dec 15 21:14:36.167 INFO [stdout] test alignment::pairwise::banded::banded::test_global_affine_ins2 ... ok Dec 15 21:14:36.167 INFO [stdout] test alignment::pairwise::banded::banded::test_insert_only_semiglobal ... ok Dec 15 21:14:36.179 INFO [stdout] test alignment::pairwise::banded::banded::test_insert_in_between_semiglobal ... ok Dec 15 21:14:36.179 INFO [stdout] test alignment::pairwise::banded::banded::test_issue11 ... ok Dec 15 21:14:36.207 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_1 ... ok Dec 15 21:14:36.213 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_2 ... ok Dec 15 21:14:36.215 INFO [stdout] test alignment::pairwise::banded::banded::test_insertion ... ok Dec 15 21:14:36.227 INFO [stdout] test alignment::pairwise::banded::banded::test_left_aligned_del ... ok Dec 15 21:14:36.227 INFO [stdout] test alignment::pairwise::banded::banded::test_left_aligned_ins ... ok Dec 15 21:14:36.231 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_3 ... ok Dec 15 21:14:36.231 INFO [stdout] test alignment::pairwise::banded::banded::test_local ... ok Dec 15 21:14:36.235 INFO [stdout] test alignment::pairwise::banded::banded::test_local_affine_ins2 ... ok Dec 15 21:14:36.243 INFO [stdout] test alignment::pairwise::banded::banded::test_longer_string_all_operations ... ok Dec 15 21:14:36.251 INFO [stdout] test alignment::pairwise::banded::banded::test_local_empty ... ok Dec 15 21:14:36.327 INFO [stdout] test alignment::pairwise::banded::banded::test_deletion ... ok Dec 15 21:14:36.359 INFO [stdout] test alignment::pairwise::banded::banded::test_band_ends_inside ... ok Dec 15 21:14:36.371 INFO [stdout] test alignment::pairwise::banded::banded::test_band_starts_inside ... ok Dec 15 21:14:36.423 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs4 ... ok Dec 15 21:14:36.459 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs3 ... ok Dec 15 21:14:36.467 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal ... ok Dec 15 21:14:36.483 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal_gap_open_lt_mismatch ... ok Dec 15 21:14:36.485 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal_simple ... ok Dec 15 21:14:36.491 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs2 ... ok Dec 15 21:14:36.519 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs5 ... ok Dec 15 21:14:36.519 INFO [stdout] test alignment::pairwise::banded::banded::test_xclip_suffix_custom ... ok Dec 15 21:14:36.535 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs1 ... ok Dec 15 21:14:36.543 INFO [stdout] test alignment::pairwise::banded::banded::test_same ... ok Dec 15 21:14:36.543 INFO [stdout] test alignment::pairwise::banded::banded::test_xclip_prefix_custom ... ok Dec 15 21:14:36.543 INFO [stdout] test alignment::pairwise::banded::banded::test_yclip_prefix_custom ... ok Dec 15 21:14:36.547 INFO [stdout] test alignment::pairwise::tests::test_aligner_new ... ok Dec 15 21:14:36.548 INFO [stdout] test alignment::pairwise::tests::test_blosum62 ... ok Dec 15 21:14:36.548 INFO [stdout] test alignment::pairwise::tests::test_global ... ok Dec 15 21:14:36.548 INFO [stdout] test alignment::pairwise::tests::test_global_affine_ins ... ok Dec 15 21:14:36.548 INFO [stdout] test alignment::pairwise::banded::banded::test_substitutions ... ok Dec 15 21:14:36.548 INFO [stdout] test alignment::pairwise::tests::test_global_right_del ... ok Dec 15 21:14:36.548 INFO [stdout] test alignment::pairwise::tests::test_insert_in_between_semiglobal ... ok Dec 15 21:14:36.551 INFO [stdout] test alignment::pairwise::tests::test_global_affine_ins2 ... ok Dec 15 21:14:36.551 INFO [stdout] test alignment::pairwise::tests::test_issue12_1 ... ok Dec 15 21:14:36.551 INFO [stdout] test alignment::pairwise::tests::test_issue11 ... ok Dec 15 21:14:36.551 INFO [stdout] test alignment::pairwise::tests::test_insert_only_semiglobal ... ok Dec 15 21:14:36.552 INFO [stdout] test alignment::pairwise::tests::test_issue12_2 ... ok Dec 15 21:14:36.559 INFO [stdout] test alignment::pairwise::tests::test_local ... ok Dec 15 21:14:36.563 INFO [stdout] test alignment::pairwise::tests::test_left_aligned_ins ... ok Dec 15 21:14:36.563 INFO [stdout] test alignment::pairwise::tests::test_local_affine_ins2 ... ok Dec 15 21:14:36.567 INFO [stdout] test alignment::pairwise::tests::test_scoring_from_scores ... ok Dec 15 21:14:36.571 INFO [stdout] test alignment::pairwise::tests::test_issue12_3 ... ok Dec 15 21:14:36.571 INFO [stdout] test alignment::pairwise::tests::test_left_aligned_del ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::pairwise::tests::test_longer_string_all_operations ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::pairwise::tests::test_semiglobal_simple ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::pairwise::tests::test_semiglobal_gap_open_lt_mismatch ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::pairwise::tests::test_xclip_suffix_custom ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::pairwise::tests::test_yclip_prefix_custom ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::pairwise::tests::test_semiglobal ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::pairwise::tests::test_yclip_suffix_custom ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::pairwise::tests::traceback_cell ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::sparse::sparse_alignment::test_expanded_matches ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::sparse::sparse_alignment::test_find_kmer_matches ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp0 ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp1 ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp2 ... ok Dec 15 21:14:36.575 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp_same ... ok Dec 15 21:14:36.583 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp ... ok Dec 15 21:14:36.619 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp2 ... ok Dec 15 21:14:36.619 INFO [stdout] test alignment::pairwise::tests::test_xclip_prefix_custom ... ok Dec 15 21:14:36.619 INFO [stdout] test alignment::pairwise::banded::banded::test_band_is_fully_inside ... ok Dec 15 21:14:36.619 INFO [stdout] test alignment::pairwise::banded::banded::test_yclip_suffix_custom ... ok Dec 15 21:14:36.619 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp1 ... ok Dec 15 21:14:36.619 INFO [stdout] test alphabets::protein::tests::number_is_no_word ... ok Dec 15 21:14:36.619 INFO [stdout] test alphabets::protein::tests::is_word ... ok Dec 15 21:14:36.619 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdpkpp_same ... ok Dec 15 21:14:36.619 INFO [stdout] test alphabets::rna::tests::is_no_word ... ok Dec 15 21:14:36.619 INFO [stdout] test alphabets::rna::tests::is_word ... ok Dec 15 21:14:36.619 INFO [stdout] test alphabets::protein::tests::symbol_is_no_word ... ok Dec 15 21:14:36.619 INFO [stdout] test alphabets::rna::tests::number_is_no_word ... ok Dec 15 21:14:36.619 INFO [stdout] test alphabets::rna::tests::symbol_is_no_word ... ok Dec 15 21:14:36.619 INFO [stdout] test alphabets::rna::tests::test_reverse_complement ... ok Dec 15 21:14:36.619 INFO [stdout] test alphabets::protein::tests::is_no_word ... ok Dec 15 21:14:36.619 INFO [stdout] test data_structures::annot_map::tests::lookup ... ok Dec 15 21:14:36.623 INFO [stdout] test data_structures::annot_map::tests::overlaps ... ok Dec 15 21:14:36.623 INFO [stdout] test data_structures::bitenc::tests::test_bitenc ... ok Dec 15 21:14:36.647 INFO [stdout] test data_structures::bit_tree::test_bit_tree::test_bit_tree ... ok Dec 15 21:14:36.647 INFO [stdout] test data_structures::bitenc::tests::test_push_values ... ok Dec 15 21:14:36.647 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdpkpp_tandem_repeat ... ok Dec 15 21:14:36.647 INFO [stdout] test data_structures::bwt::tests::test_invert_bwt ... ok Dec 15 21:14:36.647 INFO [stdout] test data_structures::bwt::tests::test_bwtfind ... ok Dec 15 21:14:36.648 INFO [stdout] test data_structures::fmindex::tests::test_fmindex ... ok Dec 15 21:14:36.648 INFO [stdout] test data_structures::bwt::tests::test_occ ... ok Dec 15 21:14:36.655 INFO [stdout] test data_structures::fmindex::tests::test_init_interval ... ok Dec 15 21:14:36.655 INFO [stdout] test data_structures::fmindex::tests::test_smems ... ok Dec 15 21:14:36.659 INFO [stdout] test data_structures::interval_tree::tests::from_iterator ... ok Dec 15 21:14:36.663 INFO [stdout] test data_structures::interval_tree::tests::iter_mut ... ok Dec 15 21:14:36.671 INFO [stdout] test data_structures::bitenc::tests::test_issue29 ... ok Dec 15 21:14:36.671 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp_tandem_repeat ... ok Dec 15 21:14:36.671 INFO [stdout] test data_structures::interval_tree::tests::test_insertion_and_intersection ... ok Dec 15 21:14:36.699 INFO [stdout] test data_structures::interval_tree::tests::zero_width_ranges ... ok Dec 15 21:14:36.699 INFO [stdout] test data_structures::qgram_index::tests::test_exact_matches ... ok Dec 15 21:14:36.707 INFO [stdout] test data_structures::qgram_index::tests::test_matches ... ok Dec 15 21:14:36.711 INFO [stdout] test data_structures::qgram_index::tests::test_exact_matches_self ... ok Dec 15 21:14:36.711 INFO [stdout] test data_structures::rank_select::tests::test_select ... ok Dec 15 21:14:36.711 INFO [stdout] test data_structures::rank_select::tests::test_single_select ... ok Dec 15 21:14:36.711 INFO [stdout] test data_structures::suffix_array::tests::test_buckets ... ok Dec 15 21:14:36.743 INFO [stdout] test alignment::distance::tests::test_hamming_dist_bad ... ok Dec 15 21:14:36.743 INFO [stdout] test data_structures::qgram_index::tests::test_qgram_matches ... ok Dec 15 21:14:36.743 INFO [stdout] test data_structures::rank_select::tests::test_rank_select ... ok Dec 15 21:14:36.743 INFO [stdout] test data_structures::suffix_array::tests::test_lms_pos ... ok Dec 15 21:14:36.755 INFO [stdout] test data_structures::suffix_array::tests::test_handles_sentinels_properly ... ok Dec 15 21:14:36.755 INFO [stdout] test data_structures::suffix_array::tests::test_pos ... ok Dec 15 21:14:36.755 INFO [stdout] test data_structures::suffix_array::tests::test_pos_types ... ok Dec 15 21:14:36.769 INFO [stdout] test data_structures::suffix_array::tests::test_issue10_1 ... ok Dec 15 21:14:36.769 INFO [stdout] test data_structures::suffix_array::tests::test_issue10_2 ... ok Dec 15 21:14:36.779 INFO [stdout] test io::bed::tests::spliced_to_bed ... ok Dec 15 21:14:36.780 INFO [stdout] test io::bed::tests::test_reader ... ok Dec 15 21:14:36.783 INFO [stdout] test io::fasta::tests::test_index_sequences ... ok Dec 15 21:14:36.786 INFO [stdout] test io::fasta::tests::test_indexed_reader ... ok Dec 15 21:14:36.795 INFO [stdout] test io::fasta::tests::test_indexed_reader_bad_reader ... ok Dec 15 21:14:36.795 INFO [stdout] test io::bed::tests::test_writer ... ok Dec 15 21:14:36.795 INFO [stdout] test io::fasta::tests::test_indexed_reader_all ... ok Dec 15 21:14:36.803 INFO [stdout] test io::fasta::tests::test_indexed_reader_by_rid_all ... ok Dec 15 21:14:36.804 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf_by_rid_all ... ok Dec 15 21:14:36.823 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter ... ok Dec 15 21:14:36.823 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf ... ok Dec 15 21:14:36.827 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf_all ... ok Dec 15 21:14:36.827 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_all ... ok Dec 15 21:14:36.831 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf_all ... ok Dec 15 21:14:36.834 INFO [stdout] test data_structures::suffix_array::tests::test_sorts_lexically ... ok Dec 15 21:14:36.851 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf ... ok Dec 15 21:14:36.851 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_read_fails ... ok Dec 15 21:14:36.851 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_by_rid_all ... ok Dec 15 21:14:36.867 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_seek_fails ... ok Dec 15 21:14:36.868 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_fetch_read_iter_fails ... ok Dec 15 21:14:36.868 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_fetch_read_fails ... ok Dec 15 21:14:36.879 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_size_hint ... ok Dec 15 21:14:36.879 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf_by_rid_all ... ok Dec 15 21:14:36.896 INFO [stdout] test io::fasta::tests::test_indexed_reader_read_read_fails ... ok Dec 15 21:14:36.896 INFO [stdout] test data_structures::fmindex::tests::test_issue39 ... ok Dec 15 21:14:36.897 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_trailing_lf ... ok Dec 15 21:14:36.898 INFO [stdout] test io::fasta::tests::test_reader ... ok Dec 15 21:14:36.899 INFO [stdout] test io::fasta::tests::test_reader_no_id ... ok Dec 15 21:14:36.900 INFO [stdout] test io::fasta::tests::test_indexed_reader_reused_buffer ... ok Dec 15 21:14:36.900 INFO [stdout] test io::fasta::tests::test_reader_wrong_header ... ok Dec 15 21:14:36.900 INFO [stdout] test io::fasta::tests::test_record_with_attrs ... ok Dec 15 21:14:36.901 INFO [stdout] test io::fasta::tests::test_reader_read_fails_iter ... ok Dec 15 21:14:36.902 INFO [stdout] test io::fasta::tests::test_writer ... ok Dec 15 21:14:36.907 INFO [stdout] test io::fastq::tests::test_reader ... ok Dec 15 21:14:36.907 INFO [stdout] test io::fasta::tests::test_indexed_reader_read_seek_fails ... ok Dec 15 21:14:36.907 INFO [stdout] test io::fasta::tests::test_reader_read_fails ... ok Dec 15 21:14:36.908 INFO [stdout] test io::fasta::tests::test_reader_non_ascii_sequence ... ok Dec 15 21:14:36.908 INFO [stdout] test io::fastq::tests::test_record_with_attrs ... ok Dec 15 21:14:36.927 INFO [stdout] test data_structures::interval_tree::tests::test_insertion_and_intersection_2 ... ok Dec 15 21:14:36.929 INFO [stdout] test io::gff::tests::test_convert_gtf2_to_gff3 ... ok Dec 15 21:14:36.943 INFO [stdout] test io::gff::tests::test_writer_gff3 ... ok Dec 15 21:14:36.943 INFO [stdout] test io::gff::tests::test_reader_gtf2_dup_attr_keys ... ok Dec 15 21:14:36.947 INFO [stdout] test pattern_matching::bndm::tests::test_find_all ... ok Dec 15 21:14:36.950 INFO [stdout] test io::gff::tests::test_reader_gtf2_2 ... ok Dec 15 21:14:36.954 INFO [stdout] test io::gff::tests::test_reader_gtf2 ... ok Dec 15 21:14:36.960 INFO [stdout] test io::gff::tests::test_reader_gff3 ... ok Dec 15 21:14:36.960 INFO [stdout] test pattern_matching::horspool::tests::test_find_all ... ok Dec 15 21:14:36.967 INFO [stdout] test io::fastq::tests::test_writer ... ok Dec 15 21:14:36.967 INFO [stdout] test pattern_matching::bom::tests::test_find_all ... ok Dec 15 21:14:36.967 INFO [stdout] test pattern_matching::bom::tests::test_delta ... ok Dec 15 21:14:36.967 INFO [stdout] test io::gff::tests::test_writer_gtf2 ... ok Dec 15 21:14:36.968 INFO [stdout] test pattern_matching::kmp::tests::test_find_all_at_start ... ok Dec 15 21:14:36.975 INFO [stdout] test pattern_matching::kmp::tests::test_find_all ... ok Dec 15 21:14:36.975 INFO [stdout] test pattern_matching::horspool::tests::test_shift ... ok Dec 15 21:14:36.975 INFO [stdout] test pattern_matching::myers::tests::test_distance ... ok Dec 15 21:14:36.976 INFO [stdout] test pattern_matching::kmp::tests::test_delta ... ok Dec 15 21:14:36.976 INFO [stdout] test pattern_matching::myers::tests::test_find_all_end ... ok Dec 15 21:14:36.977 INFO [stdout] test pattern_matching::myers::tests::test_large_dist ... ok Dec 15 21:14:36.983 INFO [stdout] test pattern_matching::myers::tests::test_full_position ... ok Dec 15 21:14:36.983 INFO [stdout] test pattern_matching::myers::tests::test_alignment ... ok Dec 15 21:14:36.983 INFO [stdout] test pattern_matching::myers::tests::test_ambig ... ok Dec 15 21:14:36.983 INFO [stdout] test pattern_matching::myers::tests::test_path_at ... ok Dec 15 21:14:36.984 INFO [stdout] test pattern_matching::myers::tests::test_find_best_end ... ok Dec 15 21:14:36.991 INFO [stdout] test pattern_matching::myers::tests::test_position_cmp ... ok Dec 15 21:14:36.991 INFO [stdout] test pattern_matching::kmp::tests::test_lps ... ok Dec 15 21:14:36.991 INFO [stdout] test pattern_matching::myers::tests::test_long_shorter ... ok Dec 15 21:14:36.998 INFO [stdout] test pattern_matching::myers::tests::test_pattern_too_long_builder ... ok Dec 15 21:14:36.999 INFO [stdout] test pattern_matching::myers::tests::test_traceback_path2 ... ok Dec 15 21:14:36.999 INFO [stdout] test pattern_matching::myers::tests::test_traceback_path ... ok Dec 15 21:14:36.999 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::find_motif ... ok Dec 15 21:14:37.000 INFO [stdout] test pattern_matching::myers::tests::test_pattern_too_long ... ok Dec 15 21:14:37.000 INFO [stdout] test pattern_matching::myers::tests::test_longest_possible ... ok Dec 15 21:14:37.000 INFO [stdout] test pattern_matching::myers::tests::test_shorter ... ok Dec 15 21:14:37.001 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_inconsist_err ... ok Dec 15 21:14:37.001 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_info_content ... ok Dec 15 21:14:37.001 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_mono_err ... ok Dec 15 21:14:37.001 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_scoring ... ok Dec 15 21:14:37.002 INFO [stdout] test pattern_matching::shift_and::tests::test_find_all ... ok Dec 15 21:14:37.002 INFO [stdout] test pattern_matching::ukkonen::tests::test_find_all_end ... ok Dec 15 21:14:37.002 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::simple_pssm ... ok Dec 15 21:14:37.003 INFO [stdout] test scores::pam120::tests::test_pam120 ... ok Dec 15 21:14:37.003 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_mono_err ... ok Dec 15 21:14:37.003 INFO [stdout] test pattern_matching::ukkonen::tests::test_find_start ... ok Dec 15 21:14:37.003 INFO [stdout] test scores::blosum62::tests::test_blosum62 ... ok Dec 15 21:14:37.015 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_inconsist_err ... ok Dec 15 21:14:37.015 INFO [stdout] test scores::pam200::tests::test_pam200 ... ok Dec 15 21:14:37.015 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_info_content ... ok Dec 15 21:14:37.016 INFO [stdout] test scores::pam250::tests::test_pam250 ... ok Dec 15 21:14:37.016 INFO [stdout] test scores::pam40::tests::test_pam40 ... ok Dec 15 21:14:37.016 INFO [stdout] test stats::combinatorics::tests::test_comb ... ok Dec 15 21:14:37.017 INFO [stdout] test seq_analysis::orf::tests::test_orf ... ok Dec 15 21:14:37.017 INFO [stdout] test stats::hmm::tests::test_discrete_viterbi_toy_example ... ok Dec 15 21:14:37.019 INFO [stdout] test stats::combinatorics::tests::test_comb_scaled ... ok Dec 15 21:14:37.019 INFO [stdout] test stats::hmm::tests::test_discrete_forward_toy_example ... ok Dec 15 21:14:37.019 INFO [stdout] test stats::hmm::tests::test_gaussian_forward_simple_example ... ok Dec 15 21:14:37.023 INFO [stdout] test stats::hmm::tests::test_gaussian_backward_simple_example ... ok Dec 15 21:14:37.023 INFO [stdout] test stats::hmm::tests::test_gaussian_viterbi_simple_example ... ok Dec 15 21:14:37.024 INFO [stdout] test stats::hmm::tests::test_gaussian_forward_equals_backward_simple_example ... ok Dec 15 21:14:37.035 INFO [stdout] test stats::bayesian::tests::test_expected_fdr ... ok Dec 15 21:14:37.035 INFO [stdout] test stats::hmm::tests::test_discrete_backward_toy_example ... ok Dec 15 21:14:37.035 INFO [stdout] test stats::pairhmm::tests::test_deletion ... ok Dec 15 21:14:37.036 INFO [stdout] test stats::pairhmm::tests::test_insertion ... ok Dec 15 21:14:37.036 INFO [stdout] test stats::probs::cdf::test::test_cdf ... ok Dec 15 21:14:37.037 INFO [stdout] test stats::pairhmm::tests::test_same ... ok Dec 15 21:14:37.043 INFO [stdout] test stats::probs::tests::test_cap_numerical_overshoot_panic ... ok Dec 15 21:14:37.043 INFO [stdout] test stats::pairhmm::tests::test_mismatch ... ok Dec 15 21:14:37.043 INFO [stdout] test stats::probs::tests::test_one_minus ... ok Dec 15 21:14:37.055 INFO [stdout] test stats::probs::tests::test_cap_numerical_overshoot ... ok Dec 15 21:14:37.055 INFO [stdout] test stats::probs::tests::test_cumsum ... ok Dec 15 21:14:37.055 INFO [stdout] test stats::probs::tests::test_simpsons_integrate ... ok Dec 15 21:14:37.056 INFO [stdout] test stats::probs::tests::test_empty_sum ... ok Dec 15 21:14:37.056 INFO [stdout] test stats::probs::tests::test_trapezoidal_integrate ... ok Dec 15 21:14:37.056 INFO [stdout] test stats::probs::tests::test_sub ... ok Dec 15 21:14:37.057 INFO [stdout] test stats::probs::tests::test_zero ... ok Dec 15 21:14:37.057 INFO [stdout] test utils::fastexp::tests::test_fastexp ... ok Dec 15 21:14:37.057 INFO [stdout] test utils::interval::tests::negative_width_range ... ok Dec 15 21:14:37.058 INFO [stdout] test utils::tests::test_prescan ... ok Dec 15 21:14:37.071 INFO [stdout] test utils::interval::tests::range_interval_conversions ... ok Dec 15 21:14:37.071 INFO [stdout] test utils::tests::test_scan ... ok Dec 15 21:14:37.072 INFO [stdout] test utils::text::tests::test_print_sequence ... ok Dec 15 21:14:37.072 INFO [stdout] test data_structures::interpolation_table::tests::test_interpolation_table ... ok Dec 15 21:14:37.087 INFO [stdout] test stats::probs::tests::test_sum ... ok Dec 15 21:14:37.087 INFO [stdout] test stats::probs::tests::test_sum_one_zero ... ok Dec 15 21:14:37.115 INFO [stdout] test stats::pairhmm::tests::test_large ... ok Dec 15 21:14:37.213 INFO [stdout] test alignment::pairwise::banded::banded::test_big ... ok Dec 15 21:14:37.319 INFO [stdout] test stats::hmm::tests::test_discrete_forward_equals_backward_toy_example ... ok Dec 15 21:14:37.319 INFO [stdout] Dec 15 21:14:37.319 INFO [stdout] test result: ok. 245 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out Dec 15 21:14:37.319 INFO [stdout] Dec 15 21:14:37.323 INFO [stderr] Doc-tests bio Dec 15 21:14:43.174 INFO [stdout] Dec 15 21:14:43.175 INFO [stdout] running 58 tests Dec 15 21:15:19.497 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::PHREDProb (line 46) ... ok Dec 15 21:15:20.251 INFO [stdout] test src/alignment/pairwise/banded.rs - alignment::pairwise::banded (line 20) ... ok Dec 15 21:15:22.866 INFO [stdout] test src/alignment/distance.rs - alignment::distance::hamming (line 16) ... ok Dec 15 21:15:24.884 INFO [stdout] test src/alignment/distance.rs - alignment::distance::levenshtein (line 48) ... ok Dec 15 21:15:26.192 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::LogProb (line 50) ... ok Dec 15 21:15:26.892 INFO [stdout] test src/alignment/sparse.rs - alignment::sparse (line 18) ... ok Dec 15 21:15:27.539 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::Prob (line 46) ... ok Dec 15 21:15:28.727 INFO [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise (line 13) ... ok Dec 15 21:16:18.478 INFO [stdout] test src/alphabets/dna.rs - alphabets::dna (line 10) ... ok Dec 15 21:16:20.251 INFO [stdout] test src/alphabets/mod.rs - alphabets (line 10) ... test src/alphabets/mod.rs - alphabets (line 10) has been running for over 60 seconds Dec 15 21:16:20.419 INFO [stdout] test src/alphabets/protein.rs - alphabets::protein (line 10) ... ok Dec 15 21:16:20.421 INFO [stdout] test src/alphabets/mod.rs - alphabets (line 10) ... ok Dec 15 21:16:24.887 INFO [stdout] test src/alphabets/rna.rs - alphabets::rna (line 10) ... test src/alphabets/rna.rs - alphabets::rna (line 10) has been running for over 60 seconds Dec 15 21:16:26.192 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::find (line 92) ... test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::find (line 92) has been running for over 60 seconds Dec 15 21:16:26.839 INFO [stdout] test src/alphabets/rna.rs - alphabets::rna (line 10) ... ok Dec 15 21:16:26.855 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::insert_at (line 58) ... ok Dec 15 21:16:27.531 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::new (line 39) ... test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::new (line 39) has been running for over 60 seconds Dec 15 21:16:28.115 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::new (line 39) ... ok Dec 15 21:16:28.731 INFO [stdout] test src/data_structures/bit_tree.rs - data_structures::bit_tree (line 12) ... test src/data_structures/bit_tree.rs - data_structures::bit_tree (line 12) has been running for over 60 seconds Dec 15 21:16:28.851 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::find (line 92) ... ok Dec 15 21:16:33.658 INFO [stdout] test src/data_structures/bit_tree.rs - data_structures::bit_tree (line 12) ... ok Dec 15 21:17:11.007 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex::FMIndexable::backward_search (line 96) ... ok Dec 15 21:17:11.359 INFO [stdout] test src/data_structures/bitenc.rs - data_structures::bitenc (line 11) ... ok Dec 15 21:17:11.359 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex (line 12) ... ok Dec 15 21:17:12.487 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex (line 32) ... ok Dec 15 21:17:15.016 INFO [stdout] test src/data_structures/bwt.rs - data_structures::bwt::bwt (line 33) ... ok Dec 15 21:17:15.167 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex::FMDIndex::smems (line 260) ... ok Dec 15 21:17:19.427 INFO [stdout] test src/data_structures/interval_tree.rs - data_structures::interval_tree (line 14) ... ok Dec 15 21:17:23.819 INFO [stdout] test src/data_structures/qgram_index.rs - data_structures::qgram_index (line 10) ... ok Dec 15 21:18:00.783 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::suffix_array (line 198) ... ok Dec 15 21:18:03.859 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::lcp (line 239) ... ok Dec 15 21:18:08.935 INFO [stdout] test src/data_structures/smallints.rs - data_structures::smallints (line 13) ... ok Dec 15 21:18:08.947 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::shortest_unique_substrings (line 304) ... ok Dec 15 21:18:09.595 INFO [stdout] test src/data_structures/rank_select.rs - data_structures::rank_select (line 11) ... ok Dec 15 21:18:10.427 INFO [stdout] test src/io/bed.rs - io::bed (line 10) ... ok Dec 15 21:18:14.267 INFO [stdout] test src/io/bed.rs - io::bed::Record (line 314) ... ok Dec 15 21:18:19.159 INFO [stdout] test src/io/bed.rs - io::bed::annot::contig::Contig::from (line 237) ... ok Dec 15 21:18:40.643 INFO [stdout] test src/io/fasta.rs - io::fasta (line 10) ... ok Dec 15 21:18:44.811 INFO [stdout] test src/io/gff.rs - io::gff (line 14) ... ok Dec 15 21:18:46.304 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::new (line 49) ... ok Dec 15 21:18:50.375 INFO [stdout] test src/lib.rs - (line 31) ... ok Dec 15 21:18:51.475 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::records (line 127) ... ok Dec 15 21:18:53.408 INFO [stdout] test src/io/fastq.rs - io::fastq (line 10) ... ok Dec 15 21:18:56.795 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::read (line 69) ... ok Dec 15 21:19:09.227 INFO [stdout] test src/lib.rs - (line 54) ... ok Dec 15 21:19:26.231 INFO [stdout] test src/pattern_matching/bndm.rs - pattern_matching::bndm (line 12) ... ok Dec 15 21:19:27.319 INFO [stdout] test src/pattern_matching/bom.rs - pattern_matching::bom (line 12) ... ok Dec 15 21:19:31.055 INFO [stdout] test src/pattern_matching/kmp.rs - pattern_matching::kmp (line 16) ... ok Dec 15 21:19:33.151 INFO [stdout] test src/pattern_matching/horspool.rs - pattern_matching::horspool (line 32) ... ok Dec 15 21:19:35.715 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::ambig (line 63) ... ok Dec 15 21:19:36.071 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::build (line 142) ... ok Dec 15 21:19:36.226 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder (line 9) ... ok Dec 15 21:19:46.551 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::text_wildcard (line 98) ... ok Dec 15 21:19:57.738 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 124) ... ok Dec 15 21:20:02.375 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 168) ... ok Dec 15 21:20:02.580 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 61) ... ok Dec 15 21:20:03.251 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 41) ... ok Dec 15 21:20:06.497 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 15) ... ok Dec 15 21:20:09.531 INFO [stdout] test src/pattern_matching/ukkonen.rs - pattern_matching::ukkonen (line 17) ... ok Dec 15 21:20:10.675 INFO [stdout] test src/pattern_matching/shift_and.rs - pattern_matching::shift_and (line 12) ... ok Dec 15 21:20:12.403 INFO [stdout] test src/seq_analysis/orf.rs - seq_analysis::orf (line 12) ... ok Dec 15 21:20:17.751 INFO [stdout] test src/stats/hmm.rs - stats::hmm (line 15) ... ok Dec 15 21:20:18.764 INFO [stdout] test src/stats/hmm.rs - stats::hmm (line 37) ... ok Dec 15 21:20:18.764 INFO [stdout] Dec 15 21:20:18.764 INFO [stdout] test result: ok. 58 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out Dec 15 21:20:18.764 INFO [stdout] Dec 15 21:20:18.840 INFO [stderr] su: No module specific data is present Dec 15 21:20:19.703 INFO running `"docker" "inspect" "02ef8da122e30b9e40238a3467f45e4a325340e6ae43cad2db8c9ae718cf44ac"` Dec 15 21:20:19.859 INFO running `"docker" "rm" "-f" "02ef8da122e30b9e40238a3467f45e4a325340e6ae43cad2db8c9ae718cf44ac"` Dec 15 21:20:20.243 INFO [stdout] 02ef8da122e30b9e40238a3467f45e4a325340e6ae43cad2db8c9ae718cf44ac