Dec 15 21:13:45.240 INFO testing bio-0.24.0 against master#bd47d6825bf4090517549d33cfef10d3300b4a75 for pr-56550 Dec 15 21:13:45.240 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56550/worker-5/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-5/pr-56550/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/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 +bd47d6825bf4090517549d33cfef10d3300b4a75-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 21:13:45.704 INFO [stdout] 6600445df21c25656449adf1510d3e102429bde7904b7cc9eb5d542e35527985 Dec 15 21:13:45.706 INFO running `"docker" "start" "-a" "6600445df21c25656449adf1510d3e102429bde7904b7cc9eb5d542e35527985"` Dec 15 21:13:47.303 INFO [stderr] usermod: no changes Dec 15 21:13:47.463 INFO [stderr] Compiling feature-probe v0.1.1 Dec 15 21:13:47.471 INFO [stderr] Compiling bio v0.24.0 (/source) Dec 15 21:13:47.471 INFO [stderr] Compiling newtype_derive v0.1.6 Dec 15 21:13:47.483 INFO [stderr] Compiling statrs v0.9.0 Dec 15 21:13:47.483 INFO [stderr] Compiling bio-types v0.4.0 Dec 15 21:13:47.483 INFO [stderr] Compiling multimap v0.4.0 Dec 15 21:13:47.483 INFO [stderr] Compiling csv v1.0.2 Dec 15 21:13:47.483 INFO [stderr] Compiling vec_map v0.8.1 Dec 15 21:13:51.587 INFO [stderr] Compiling bv v0.10.0 Dec 15 21:14:08.014 INFO [stderr] warning: unused import: `std::ops::Deref` Dec 15 21:14:08.014 INFO [stderr] --> src/data_structures/bwt.rs:15:5 Dec 15 21:14:08.014 INFO [stderr] | Dec 15 21:14:08.014 INFO [stderr] 15 | use std::ops::Deref; Dec 15 21:14:08.014 INFO [stderr] | ^^^^^^^^^^^^^^^ Dec 15 21:14:08.014 INFO [stderr] | Dec 15 21:14:08.014 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 15 21:14:08.014 INFO [stderr] Dec 15 21:14:10.111 INFO [stderr] warning: use of deprecated item 'ndarray::impl_methods::>::subview': renamed to `index_axis` Dec 15 21:14:10.111 INFO [stderr] --> src/stats/hmm.rs:266:22 Dec 15 21:14:10.111 INFO [stderr] | Dec 15 21:14:10.111 INFO [stderr] 266 | .subview(Axis(0), i - 1) Dec 15 21:14:10.111 INFO [stderr] | ^^^^^^^ Dec 15 21:14:10.111 INFO [stderr] | Dec 15 21:14:10.111 INFO [stderr] = note: #[warn(deprecated)] on by default Dec 15 21:14:10.111 INFO [stderr] Dec 15 21:14:15.958 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 28.64s Dec 15 21:14:15.965 INFO [stderr] su: No module specific data is present Dec 15 21:14:16.792 INFO running `"docker" "inspect" "6600445df21c25656449adf1510d3e102429bde7904b7cc9eb5d542e35527985"` Dec 15 21:14:16.965 INFO running `"docker" "rm" "-f" "6600445df21c25656449adf1510d3e102429bde7904b7cc9eb5d542e35527985"` Dec 15 21:14:17.250 INFO [stdout] 6600445df21c25656449adf1510d3e102429bde7904b7cc9eb5d542e35527985 Dec 15 21:14:17.259 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56550/worker-5/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-5/pr-56550/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/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 +bd47d6825bf4090517549d33cfef10d3300b4a75-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 21:14:17.702 INFO [stdout] 375829dec84af84f6d0933d325dc31b826527c3ee1df7b7d08738281bc265f5c Dec 15 21:14:17.708 INFO running `"docker" "start" "-a" "375829dec84af84f6d0933d325dc31b826527c3ee1df7b7d08738281bc265f5c"` Dec 15 21:14:18.810 INFO [stderr] usermod: no changes Dec 15 21:14:18.979 INFO [stderr] Compiling bio v0.24.0 (/source) Dec 15 21:14:23.299 INFO [stderr] warning: unused import: `std::ops::Deref` Dec 15 21:14:23.299 INFO [stderr] --> src/data_structures/bwt.rs:15:5 Dec 15 21:14:23.299 INFO [stderr] | Dec 15 21:14:23.299 INFO [stderr] 15 | use std::ops::Deref; Dec 15 21:14:23.299 INFO [stderr] | ^^^^^^^^^^^^^^^ Dec 15 21:14:23.299 INFO [stderr] | Dec 15 21:14:23.308 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 15 21:14:23.308 INFO [stderr] Dec 15 21:14:26.979 INFO [stderr] warning: use of deprecated item 'ndarray::impl_methods::>::subview': renamed to `index_axis` Dec 15 21:14:26.979 INFO [stderr] --> src/stats/hmm.rs:266:22 Dec 15 21:14:26.979 INFO [stderr] | Dec 15 21:14:26.979 INFO [stderr] 266 | .subview(Axis(0), i - 1) Dec 15 21:14:26.979 INFO [stderr] | ^^^^^^^ Dec 15 21:14:26.979 INFO [stderr] | Dec 15 21:14:26.979 INFO [stderr] = note: #[warn(deprecated)] on by default Dec 15 21:14:26.979 INFO [stderr] Dec 15 21:14:44.403 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 25.57s Dec 15 21:14:44.407 INFO [stderr] su: No module specific data is present Dec 15 21:14:44.861 INFO running `"docker" "inspect" "375829dec84af84f6d0933d325dc31b826527c3ee1df7b7d08738281bc265f5c"` Dec 15 21:14:45.111 INFO running `"docker" "rm" "-f" "375829dec84af84f6d0933d325dc31b826527c3ee1df7b7d08738281bc265f5c"` Dec 15 21:14:45.406 INFO [stdout] 375829dec84af84f6d0933d325dc31b826527c3ee1df7b7d08738281bc265f5c Dec 15 21:14:45.409 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56550/worker-5/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-5/pr-56550/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/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 +bd47d6825bf4090517549d33cfef10d3300b4a75-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 21:14:45.743 INFO [stdout] 6950bdd1f9d7a5057f2f68266ca24138a68cc36c8e59f5cd8401875560bd6a69 Dec 15 21:14:45.748 INFO running `"docker" "start" "-a" "6950bdd1f9d7a5057f2f68266ca24138a68cc36c8e59f5cd8401875560bd6a69"` Dec 15 21:14:47.383 INFO [stderr] usermod: no changes Dec 15 21:14:47.567 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 0.15s Dec 15 21:14:47.575 INFO [stderr] Running /target/debug/deps/bio-7ab7a5356e5615ef Dec 15 21:14:47.575 INFO [stdout] Dec 15 21:14:47.575 INFO [stdout] running 245 tests Dec 15 21:14:47.575 INFO [stdout] test alignment::pairwise::banded::banded::test_band_add_kmer ... ok Dec 15 21:14:47.575 INFO [stdout] test alignment::pairwise::banded::banded::test_band_add_entry ... ok Dec 15 21:14:47.575 INFO [stdout] test alignment::distance::tests::test_hamming_dist_good ... ok Dec 15 21:14:47.575 INFO [stdout] test alignment::distance::tests::test_levenshtein_dist ... ok Dec 15 21:14:47.635 INFO [stdout] test alignment::pairwise::banded::banded::test_blosum62 ... ok Dec 15 21:14:47.635 INFO [stdout] test alignment::pairwise::banded::banded::test_aligner_new ... ok Dec 15 21:14:47.635 INFO [stdout] test alignment::pairwise::banded::banded::test_global ... ok Dec 15 21:14:47.635 INFO [stdout] test alignment::pairwise::banded::banded::test_global_affine_ins ... ok Dec 15 21:14:47.643 INFO [stdout] test alignment::pairwise::banded::banded::test_global_right_del ... ok Dec 15 21:14:47.643 INFO [stdout] test alignment::pairwise::banded::banded::test_global_affine_ins2 ... ok Dec 15 21:14:47.643 INFO [stdout] test alignment::pairwise::banded::banded::test_insert_only_semiglobal ... ok Dec 15 21:14:47.643 INFO [stdout] test alignment::pairwise::banded::banded::test_insert_in_between_semiglobal ... ok Dec 15 21:14:47.643 INFO [stdout] test alignment::pairwise::banded::banded::test_issue11 ... ok Dec 15 21:14:47.647 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_1 ... ok Dec 15 21:14:47.647 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_2 ... ok Dec 15 21:14:47.647 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_3 ... ok Dec 15 21:14:47.647 INFO [stdout] test alignment::pairwise::banded::banded::test_left_aligned_del ... ok Dec 15 21:14:47.647 INFO [stdout] test alignment::pairwise::banded::banded::test_left_aligned_ins ... ok Dec 15 21:14:47.647 INFO [stdout] test alignment::pairwise::banded::banded::test_local ... ok Dec 15 21:14:47.683 INFO [stdout] test alignment::pairwise::banded::banded::test_local_affine_ins2 ... ok Dec 15 21:14:47.683 INFO [stdout] test alignment::pairwise::banded::banded::test_insertion ... ok Dec 15 21:14:47.683 INFO [stdout] test alignment::pairwise::banded::banded::test_longer_string_all_operations ... ok Dec 15 21:14:47.683 INFO [stdout] test alignment::pairwise::banded::banded::test_local_empty ... ok Dec 15 21:14:47.755 INFO [stdout] test alignment::pairwise::banded::banded::test_band_ends_inside ... ok Dec 15 21:14:47.811 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs1 ... ok Dec 15 21:14:47.811 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs2 ... ok Dec 15 21:14:47.831 INFO [stdout] test alignment::pairwise::banded::banded::test_band_starts_inside ... ok Dec 15 21:14:47.867 INFO [stdout] test alignment::pairwise::banded::banded::test_deletion ... ok Dec 15 21:14:47.894 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal ... ok Dec 15 21:14:47.903 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs3 ... ok Dec 15 21:14:47.908 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal_gap_open_lt_mismatch ... ok Dec 15 21:14:47.939 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal_simple ... ok Dec 15 21:14:47.940 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs5 ... ok Dec 15 21:14:47.940 INFO [stdout] test alignment::pairwise::banded::banded::test_xclip_prefix_custom ... ok Dec 15 21:14:47.944 INFO [stdout] test alignment::pairwise::banded::banded::test_xclip_suffix_custom ... ok Dec 15 21:14:47.979 INFO [stdout] test alignment::pairwise::banded::banded::test_yclip_prefix_custom ... ok Dec 15 21:14:47.979 INFO [stdout] test alignment::pairwise::banded::banded::test_yclip_suffix_custom ... ok Dec 15 21:14:47.987 INFO [stdout] test alignment::pairwise::tests::test_aligner_new ... ok Dec 15 21:14:47.987 INFO [stdout] test alignment::pairwise::tests::test_blosum62 ... ok Dec 15 21:14:47.995 INFO [stdout] test alignment::pairwise::tests::test_global ... ok Dec 15 21:14:47.995 INFO [stdout] test alignment::pairwise::tests::test_global_affine_ins ... ok Dec 15 21:14:47.996 INFO [stdout] test alignment::pairwise::tests::test_global_affine_ins2 ... ok Dec 15 21:14:47.996 INFO [stdout] test alignment::pairwise::tests::test_insert_in_between_semiglobal ... ok Dec 15 21:14:47.997 INFO [stdout] test alignment::pairwise::tests::test_global_right_del ... ok Dec 15 21:14:48.007 INFO [stdout] test alignment::pairwise::tests::test_insert_only_semiglobal ... ok Dec 15 21:14:48.007 INFO [stdout] test alignment::pairwise::tests::test_issue11 ... ok Dec 15 21:14:48.007 INFO [stdout] test alignment::pairwise::tests::test_issue12_1 ... ok Dec 15 21:14:48.015 INFO [stdout] test alignment::pairwise::tests::test_issue12_3 ... ok Dec 15 21:14:48.015 INFO [stdout] test alignment::pairwise::tests::test_left_aligned_del ... ok Dec 15 21:14:48.015 INFO [stdout] test alignment::pairwise::tests::test_left_aligned_ins ... ok Dec 15 21:14:48.016 INFO [stdout] test alignment::pairwise::tests::test_local ... ok Dec 15 21:14:48.017 INFO [stdout] test alignment::pairwise::tests::test_local_affine_ins2 ... ok Dec 15 21:14:48.031 INFO [stdout] test alignment::pairwise::tests::test_longer_string_all_operations ... ok Dec 15 21:14:48.031 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs4 ... ok Dec 15 21:14:48.031 INFO [stdout] test alignment::pairwise::tests::test_scoring_from_scores ... ok Dec 15 21:14:48.031 INFO [stdout] test alignment::pairwise::tests::test_semiglobal ... ok Dec 15 21:14:48.039 INFO [stdout] test alignment::pairwise::tests::test_semiglobal_gap_open_lt_mismatch ... ok Dec 15 21:14:48.039 INFO [stdout] test alignment::pairwise::tests::test_semiglobal_simple ... ok Dec 15 21:14:48.051 INFO [stdout] test alignment::pairwise::tests::test_xclip_prefix_custom ... ok Dec 15 21:14:48.051 INFO [stdout] test alignment::pairwise::tests::test_xclip_suffix_custom ... ok Dec 15 21:14:48.051 INFO [stdout] test alignment::pairwise::tests::test_yclip_prefix_custom ... ok Dec 15 21:14:48.051 INFO [stdout] test alignment::pairwise::tests::test_issue12_2 ... ok Dec 15 21:14:48.059 INFO [stdout] test alignment::pairwise::tests::test_yclip_suffix_custom ... ok Dec 15 21:14:48.059 INFO [stdout] test alignment::pairwise::tests::traceback_cell ... ok Dec 15 21:14:48.059 INFO [stdout] test alignment::sparse::sparse_alignment::test_expanded_matches ... ok Dec 15 21:14:48.067 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp1 ... ok Dec 15 21:14:48.067 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp0 ... ok Dec 15 21:14:48.071 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp2 ... ok Dec 15 21:14:48.078 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp_same ... ok Dec 15 21:14:48.083 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp ... ok Dec 15 21:14:48.095 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp1 ... ok Dec 15 21:14:48.095 INFO [stdout] test alignment::pairwise::banded::banded::test_same ... ok Dec 15 21:14:48.095 INFO [stdout] test alignment::sparse::sparse_alignment::test_find_kmer_matches ... ok Dec 15 21:14:48.096 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp2 ... ok Dec 15 21:14:48.116 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdpkpp_same ... ok Dec 15 21:14:48.116 INFO [stdout] test alphabets::protein::tests::is_no_word ... ok Dec 15 21:14:48.116 INFO [stdout] test alphabets::protein::tests::is_word ... ok Dec 15 21:14:48.116 INFO [stdout] test alphabets::protein::tests::symbol_is_no_word ... ok Dec 15 21:14:48.117 INFO [stdout] test alignment::pairwise::banded::banded::test_band_is_fully_inside ... ok Dec 15 21:14:48.138 INFO [stdout] test alignment::pairwise::banded::banded::test_substitutions ... ok Dec 15 21:14:48.138 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp_tandem_repeat ... ok Dec 15 21:14:48.138 INFO [stdout] test alphabets::protein::tests::number_is_no_word ... ok Dec 15 21:14:48.138 INFO [stdout] test alphabets::rna::tests::is_no_word ... ok Dec 15 21:14:48.138 INFO [stdout] test alphabets::rna::tests::is_word ... ok Dec 15 21:14:48.138 INFO [stdout] test alphabets::rna::tests::symbol_is_no_word ... ok Dec 15 21:14:48.138 INFO [stdout] test data_structures::annot_map::tests::overlaps ... ok Dec 15 21:14:48.139 INFO [stdout] test alphabets::rna::tests::test_reverse_complement ... ok Dec 15 21:14:48.139 INFO [stdout] test data_structures::annot_map::tests::lookup ... ok Dec 15 21:14:48.139 INFO [stdout] test alphabets::rna::tests::number_is_no_word ... ok Dec 15 21:14:48.139 INFO [stdout] test data_structures::bit_tree::test_bit_tree::test_bit_tree ... ok Dec 15 21:14:48.139 INFO [stdout] test data_structures::bitenc::tests::test_bitenc ... ok Dec 15 21:14:48.159 INFO [stdout] test data_structures::bwt::tests::test_invert_bwt ... ok Dec 15 21:14:48.159 INFO [stdout] test data_structures::bwt::tests::test_bwtfind ... ok Dec 15 21:14:48.159 INFO [stdout] test data_structures::bitenc::tests::test_push_values ... ok Dec 15 21:14:48.159 INFO [stdout] test data_structures::bitenc::tests::test_issue29 ... ok Dec 15 21:14:48.161 INFO [stdout] test alignment::distance::tests::test_hamming_dist_bad ... ok Dec 15 21:14:48.167 INFO [stdout] test data_structures::fmindex::tests::test_smems ... ok Dec 15 21:14:48.167 INFO [stdout] test data_structures::bwt::tests::test_occ ... ok Dec 15 21:14:48.167 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdpkpp_tandem_repeat ... ok Dec 15 21:14:48.167 INFO [stdout] test data_structures::fmindex::tests::test_fmindex ... ok Dec 15 21:14:48.167 INFO [stdout] test data_structures::interval_tree::tests::from_iterator ... ok Dec 15 21:14:48.180 INFO [stdout] test data_structures::interval_tree::tests::iter_mut ... ok Dec 15 21:14:48.180 INFO [stdout] test data_structures::interval_tree::tests::test_insertion_and_intersection ... ok Dec 15 21:14:48.180 INFO [stdout] test data_structures::fmindex::tests::test_init_interval ... ok Dec 15 21:14:48.180 INFO [stdout] test data_structures::qgram_index::tests::test_exact_matches_self ... ok Dec 15 21:14:48.181 INFO [stdout] test data_structures::qgram_index::tests::test_exact_matches ... ok Dec 15 21:14:48.181 INFO [stdout] test data_structures::interval_tree::tests::zero_width_ranges ... ok Dec 15 21:14:48.183 INFO [stdout] test data_structures::rank_select::tests::test_select ... ok Dec 15 21:14:48.183 INFO [stdout] test data_structures::rank_select::tests::test_rank_select ... ok Dec 15 21:14:48.191 INFO [stdout] test data_structures::qgram_index::tests::test_qgram_matches ... ok Dec 15 21:14:48.199 INFO [stdout] test data_structures::qgram_index::tests::test_matches ... ok Dec 15 21:14:48.211 INFO [stdout] test data_structures::suffix_array::tests::test_issue10_1 ... ok Dec 15 21:14:48.211 INFO [stdout] test data_structures::suffix_array::tests::test_buckets ... ok Dec 15 21:14:48.219 INFO [stdout] test data_structures::suffix_array::tests::test_lms_pos ... ok Dec 15 21:14:48.219 INFO [stdout] test data_structures::suffix_array::tests::test_issue10_2 ... ok Dec 15 21:14:48.219 INFO [stdout] test data_structures::suffix_array::tests::test_pos ... ok Dec 15 21:14:48.220 INFO [stdout] test data_structures::suffix_array::tests::test_pos_types ... ok Dec 15 21:14:48.231 INFO [stdout] test io::bed::tests::spliced_to_bed ... ok Dec 15 21:14:48.232 INFO [stdout] test io::bed::tests::test_reader ... ok Dec 15 21:14:48.243 INFO [stdout] test data_structures::suffix_array::tests::test_handles_sentinels_properly ... ok Dec 15 21:14:48.252 INFO [stdout] test io::fasta::tests::test_index_sequences ... ok Dec 15 21:14:48.252 INFO [stdout] test io::bed::tests::test_writer ... ok Dec 15 21:14:48.255 INFO [stdout] test io::fasta::tests::test_indexed_reader_all ... ok Dec 15 21:14:48.256 INFO [stdout] test data_structures::rank_select::tests::test_single_select ... ok Dec 15 21:14:48.258 INFO [stdout] test io::fasta::tests::test_indexed_reader ... ok Dec 15 21:14:48.275 INFO [stdout] test io::fasta::tests::test_indexed_reader_by_rid_all ... ok Dec 15 21:14:48.275 INFO [stdout] test io::fasta::tests::test_indexed_reader_bad_reader ... ok Dec 15 21:14:48.291 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf_by_rid_all ... ok Dec 15 21:14:48.291 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf_all ... ok Dec 15 21:14:48.295 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf ... ok Dec 15 21:14:48.295 INFO [stdout] test data_structures::suffix_array::tests::test_sorts_lexically ... ok Dec 15 21:14:48.303 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_by_rid_all ... ok Dec 15 21:14:48.323 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter ... ok Dec 15 21:14:48.323 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_all ... ok Dec 15 21:14:48.323 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf_all ... ok Dec 15 21:14:48.323 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf ... ok Dec 15 21:14:48.340 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_read_fails ... ok Dec 15 21:14:48.347 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf_by_rid_all ... ok Dec 15 21:14:48.347 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_size_hint ... ok Dec 15 21:14:48.348 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_seek_fails ... ok Dec 15 21:14:48.348 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_fetch_read_fails ... ok Dec 15 21:14:48.349 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_fetch_read_iter_fails ... ok Dec 15 21:14:48.349 INFO [stdout] test io::fasta::tests::test_indexed_reader_read_read_fails ... ok Dec 15 21:14:48.351 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_trailing_lf ... ok Dec 15 21:14:48.355 INFO [stdout] test io::fasta::tests::test_indexed_reader_read_seek_fails ... ok Dec 15 21:14:48.356 INFO [stdout] test io::fasta::tests::test_reader ... ok Dec 15 21:14:48.356 INFO [stdout] test io::fasta::tests::test_indexed_reader_reused_buffer ... ok Dec 15 21:14:48.357 INFO [stdout] test io::fasta::tests::test_reader_no_id ... ok Dec 15 21:14:48.371 INFO [stdout] test io::fasta::tests::test_reader_non_ascii_sequence ... ok Dec 15 21:14:48.375 INFO [stdout] test io::fasta::tests::test_reader_read_fails ... ok Dec 15 21:14:48.375 INFO [stdout] test io::fasta::tests::test_reader_wrong_header ... ok Dec 15 21:14:48.375 INFO [stdout] test io::fasta::tests::test_reader_read_fails_iter ... ok Dec 15 21:14:48.387 INFO [stdout] test io::fastq::tests::test_reader ... ok Dec 15 21:14:48.387 INFO [stdout] test io::fasta::tests::test_record_with_attrs ... ok Dec 15 21:14:48.387 INFO [stdout] test io::fasta::tests::test_writer ... ok Dec 15 21:14:48.387 INFO [stdout] test io::fastq::tests::test_record_with_attrs ... ok Dec 15 21:14:48.388 INFO [stdout] test io::fastq::tests::test_writer ... ok Dec 15 21:14:48.411 INFO [stdout] test io::gff::tests::test_reader_gtf2_2 ... ok Dec 15 21:14:48.414 INFO [stdout] test io::gff::tests::test_reader_gtf2 ... ok Dec 15 21:14:48.417 INFO [stdout] test io::gff::tests::test_reader_gff3 ... ok Dec 15 21:14:48.435 INFO [stdout] test io::gff::tests::test_convert_gtf2_to_gff3 ... ok Dec 15 21:14:48.436 INFO [stdout] test io::gff::tests::test_reader_gtf2_dup_attr_keys ... ok Dec 15 21:14:48.437 INFO [stdout] test data_structures::fmindex::tests::test_issue39 ... ok Dec 15 21:14:48.437 INFO [stdout] test pattern_matching::bndm::tests::test_find_all ... ok Dec 15 21:14:48.443 INFO [stdout] test pattern_matching::horspool::tests::test_find_all ... ok Dec 15 21:14:48.443 INFO [stdout] test pattern_matching::bom::tests::test_delta ... ok Dec 15 21:14:48.445 INFO [stdout] test io::gff::tests::test_writer_gtf2 ... ok Dec 15 21:14:48.445 INFO [stdout] test pattern_matching::bom::tests::test_find_all ... ok Dec 15 21:14:48.446 INFO [stdout] test pattern_matching::kmp::tests::test_delta ... ok Dec 15 21:14:48.459 INFO [stdout] test pattern_matching::kmp::tests::test_find_all_at_start ... ok Dec 15 21:14:48.459 INFO [stdout] test pattern_matching::horspool::tests::test_shift ... ok Dec 15 21:14:48.459 INFO [stdout] test pattern_matching::kmp::tests::test_lps ... ok Dec 15 21:14:48.459 INFO [stdout] test pattern_matching::myers::tests::test_alignment ... ok Dec 15 21:14:48.459 INFO [stdout] test pattern_matching::myers::tests::test_ambig ... ok Dec 15 21:14:48.460 INFO [stdout] test pattern_matching::myers::tests::test_find_all_end ... ok Dec 15 21:14:48.460 INFO [stdout] test pattern_matching::myers::tests::test_find_best_end ... ok Dec 15 21:14:48.460 INFO [stdout] test pattern_matching::myers::tests::test_full_position ... ok Dec 15 21:14:48.460 INFO [stdout] test pattern_matching::myers::tests::test_distance ... ok Dec 15 21:14:48.471 INFO [stdout] test io::gff::tests::test_writer_gff3 ... ok Dec 15 21:14:48.471 INFO [stdout] test pattern_matching::kmp::tests::test_find_all ... ok Dec 15 21:14:48.472 INFO [stdout] test pattern_matching::myers::tests::test_large_dist ... ok Dec 15 21:14:48.472 INFO [stdout] test pattern_matching::myers::tests::test_long_shorter ... ok Dec 15 21:14:48.472 INFO [stdout] test pattern_matching::myers::tests::test_longest_possible ... ok Dec 15 21:14:48.472 INFO [stdout] test pattern_matching::myers::tests::test_path_at ... ok Dec 15 21:14:48.483 INFO [stdout] test pattern_matching::myers::tests::test_shorter ... ok Dec 15 21:14:48.483 INFO [stdout] test pattern_matching::myers::tests::test_traceback_path ... ok Dec 15 21:14:48.483 INFO [stdout] test pattern_matching::myers::tests::test_position_cmp ... ok Dec 15 21:14:48.503 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::find_motif ... ok Dec 15 21:14:48.503 INFO [stdout] test pattern_matching::myers::tests::test_traceback_path2 ... ok Dec 15 21:14:48.504 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::simple_pssm ... ok Dec 15 21:14:48.530 INFO [stdout] test data_structures::interval_tree::tests::test_insertion_and_intersection_2 ... ok Dec 15 21:14:48.530 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_info_content ... ok Dec 15 21:14:48.530 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_mono_err ... ok Dec 15 21:14:48.531 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_inconsist_err ... ok Dec 15 21:14:48.531 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_inconsist_err ... ok Dec 15 21:14:48.539 INFO [stdout] test pattern_matching::myers::tests::test_pattern_too_long ... ok Dec 15 21:14:48.539 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_info_content ... ok Dec 15 21:14:48.539 INFO [stdout] test pattern_matching::shift_and::tests::test_find_all ... ok Dec 15 21:14:48.543 INFO [stdout] test scores::blosum62::tests::test_blosum62 ... ok Dec 15 21:14:48.544 INFO [stdout] test pattern_matching::ukkonen::tests::test_find_start ... ok Dec 15 21:14:48.544 INFO [stdout] test pattern_matching::ukkonen::tests::test_find_all_end ... ok Dec 15 21:14:48.544 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_mono_err ... ok Dec 15 21:14:48.547 INFO [stdout] test scores::pam120::tests::test_pam120 ... ok Dec 15 21:14:48.547 INFO [stdout] test scores::pam250::tests::test_pam250 ... ok Dec 15 21:14:48.547 INFO [stdout] test scores::pam200::tests::test_pam200 ... ok Dec 15 21:14:48.548 INFO [stdout] test seq_analysis::orf::tests::test_orf ... ok Dec 15 21:14:48.548 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_scoring ... ok Dec 15 21:14:48.559 INFO [stdout] test stats::combinatorics::tests::test_comb ... ok Dec 15 21:14:48.559 INFO [stdout] test stats::combinatorics::tests::test_comb_scaled ... ok Dec 15 21:14:48.560 INFO [stdout] test stats::bayesian::tests::test_expected_fdr ... ok Dec 15 21:14:48.567 INFO [stdout] test scores::pam40::tests::test_pam40 ... ok Dec 15 21:14:48.571 INFO [stdout] test stats::hmm::tests::test_discrete_forward_toy_example ... ok Dec 15 21:14:48.571 INFO [stdout] test stats::hmm::tests::test_gaussian_backward_simple_example ... ok Dec 15 21:14:48.571 INFO [stdout] test stats::hmm::tests::test_gaussian_forward_simple_example ... ok Dec 15 21:14:48.571 INFO [stdout] test stats::hmm::tests::test_gaussian_viterbi_simple_example ... ok Dec 15 21:14:48.579 INFO [stdout] test stats::hmm::tests::test_discrete_viterbi_toy_example ... ok Dec 15 21:14:48.587 INFO [stdout] test stats::hmm::tests::test_gaussian_forward_equals_backward_simple_example ... ok Dec 15 21:14:48.587 INFO [stdout] test stats::pairhmm::tests::test_deletion ... ok Dec 15 21:14:48.591 INFO [stdout] test pattern_matching::myers::tests::test_pattern_too_long_builder ... ok Dec 15 21:14:48.591 INFO [stdout] test stats::hmm::tests::test_discrete_backward_toy_example ... ok Dec 15 21:14:48.591 INFO [stdout] test stats::pairhmm::tests::test_insertion ... ok Dec 15 21:14:48.591 INFO [stdout] test stats::probs::tests::test_cap_numerical_overshoot ... ok Dec 15 21:14:48.595 INFO [stdout] test stats::pairhmm::tests::test_mismatch ... ok Dec 15 21:14:48.599 INFO [stdout] test stats::probs::tests::test_cumsum ... ok Dec 15 21:14:48.599 INFO [stdout] test stats::probs::tests::test_empty_sum ... ok Dec 15 21:14:48.599 INFO [stdout] test stats::probs::cdf::test::test_cdf ... ok Dec 15 21:14:48.599 INFO [stdout] test stats::pairhmm::tests::test_same ... ok Dec 15 21:14:48.614 INFO [stdout] test stats::probs::tests::test_cap_numerical_overshoot_panic ... ok Dec 15 21:14:48.619 INFO [stdout] test stats::probs::tests::test_sub ... ok Dec 15 21:14:48.635 INFO [stdout] test stats::probs::tests::test_simpsons_integrate ... ok Dec 15 21:14:48.643 INFO [stdout] test stats::probs::tests::test_sum ... ok Dec 15 21:14:48.643 INFO [stdout] test stats::probs::tests::test_sum_one_zero ... ok Dec 15 21:14:48.643 INFO [stdout] test utils::fastexp::tests::test_fastexp ... ok Dec 15 21:14:48.644 INFO [stdout] test utils::interval::tests::negative_width_range ... ok Dec 15 21:14:48.644 INFO [stdout] test utils::interval::tests::range_interval_conversions ... ok Dec 15 21:14:48.644 INFO [stdout] test utils::tests::test_prescan ... ok Dec 15 21:14:48.644 INFO [stdout] test utils::tests::test_scan ... ok Dec 15 21:14:48.651 INFO [stdout] test stats::probs::tests::test_one_minus ... ok Dec 15 21:14:48.651 INFO [stdout] test utils::text::tests::test_print_sequence ... ok Dec 15 21:14:48.651 INFO [stdout] test stats::probs::tests::test_zero ... ok Dec 15 21:14:48.675 INFO [stdout] test stats::probs::tests::test_trapezoidal_integrate ... ok Dec 15 21:14:48.679 INFO [stdout] test stats::pairhmm::tests::test_large ... ok Dec 15 21:14:48.719 INFO [stdout] test data_structures::interpolation_table::tests::test_interpolation_table ... ok Dec 15 21:14:48.805 INFO [stdout] test alignment::pairwise::banded::banded::test_big ... ok Dec 15 21:14:48.817 INFO [stdout] test stats::hmm::tests::test_discrete_forward_equals_backward_toy_example ... ok Dec 15 21:14:48.817 INFO [stdout] Dec 15 21:14:48.817 INFO [stdout] test result: ok. 245 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out Dec 15 21:14:48.817 INFO [stdout] Dec 15 21:14:48.821 INFO [stderr] Doc-tests bio Dec 15 21:14:54.839 INFO [stdout] Dec 15 21:14:54.839 INFO [stdout] running 58 tests Dec 15 21:15:39.274 INFO [stdout] test src/alignment/sparse.rs - alignment::sparse (line 18) ... ok Dec 15 21:15:43.495 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::Prob (line 46) ... ok Dec 15 21:15:44.114 INFO [stdout] test src/alignment/distance.rs - alignment::distance::hamming (line 16) ... ok Dec 15 21:15:45.626 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::PHREDProb (line 46) ... ok Dec 15 21:15:48.527 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::LogProb (line 50) ... ok Dec 15 21:15:51.566 INFO [stdout] test src/alignment/distance.rs - alignment::distance::levenshtein (line 48) ... ok Dec 15 21:15:51.599 INFO [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise (line 13) ... ok Dec 15 21:15:54.723 INFO [stdout] test src/alignment/pairwise/banded.rs - alignment::pairwise::banded (line 20) ... ok Dec 15 21:16:39.279 INFO [stdout] test src/alphabets/dna.rs - alphabets::dna (line 10) ... test src/alphabets/dna.rs - alphabets::dna (line 10) has been running for over 60 seconds Dec 15 21:16:39.775 INFO [stdout] test src/alphabets/dna.rs - alphabets::dna (line 10) ... ok Dec 15 21:16:40.311 INFO [stdout] test src/alphabets/protein.rs - alphabets::protein (line 10) ... ok Dec 15 21:16:43.046 INFO [stdout] test src/alphabets/rna.rs - alphabets::rna (line 10) ... ok Dec 15 21:16:43.452 INFO [stdout] test src/alphabets/mod.rs - alphabets (line 10) ... ok Dec 15 21:16:45.399 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::insert_at (line 58) ... ok Dec 15 21:16:47.028 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::new (line 39) ... ok Dec 15 21:16:47.131 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::find (line 92) ... ok Dec 15 21:16:54.735 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 21:16:54.735 INFO [stdout] test src/data_structures/bit_tree.rs - data_structures::bit_tree (line 12) ... ok Dec 15 21:17:27.163 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex (line 32) ... ok Dec 15 21:17:32.798 INFO [stdout] test src/data_structures/bitenc.rs - data_structures::bitenc (line 11) ... ok Dec 15 21:17:34.311 INFO [stdout] test src/data_structures/bwt.rs - data_structures::bwt::bwt (line 33) ... ok Dec 15 21:17:34.976 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex::FMIndexable::backward_search (line 96) ... ok Dec 15 21:17:42.995 INFO [stdout] test src/data_structures/interval_tree.rs - data_structures::interval_tree (line 14) ... ok Dec 15 21:17:43.051 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex (line 12) ... test src/data_structures/fmindex.rs - data_structures::fmindex (line 12) has been running for over 60 seconds Dec 15 21:17:43.436 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex (line 12) ... ok Dec 15 21:17:44.527 INFO [stdout] test src/data_structures/qgram_index.rs - data_structures::qgram_index (line 10) ... ok Dec 15 21:17:45.411 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 15 21:17:46.107 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex::FMDIndex::smems (line 260) ... ok Dec 15 21:18:13.083 INFO [stdout] test src/data_structures/rank_select.rs - data_structures::rank_select (line 11) ... ok Dec 15 21:18:28.375 INFO [stdout] test src/data_structures/smallints.rs - data_structures::smallints (line 13) ... ok Dec 15 21:18:31.627 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::shortest_unique_substrings (line 304) ... ok Dec 15 21:18:32.813 INFO [stdout] test src/io/bed.rs - io::bed (line 10) ... ok Dec 15 21:18:33.055 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::lcp (line 239) ... ok Dec 15 21:18:33.587 INFO [stdout] test src/io/bed.rs - io::bed::annot::contig::Contig::from (line 237) ... ok Dec 15 21:18:36.142 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::suffix_array (line 198) ... ok Dec 15 21:18:37.099 INFO [stdout] test src/io/bed.rs - io::bed::Record (line 314) ... ok Dec 15 21:18:55.415 INFO [stdout] test src/io/fasta.rs - io::fasta (line 10) ... ok Dec 15 21:19:10.491 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::new (line 49) ... ok Dec 15 21:19:13.727 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::read (line 69) ... ok Dec 15 21:19:14.507 INFO [stdout] test src/io/gff.rs - io::gff (line 14) ... ok Dec 15 21:19:14.831 INFO [stdout] test src/io/fastq.rs - io::fastq (line 10) ... ok Dec 15 21:19:17.091 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::records (line 127) ... ok Dec 15 21:19:17.603 INFO [stdout] test src/lib.rs - (line 54) ... ok Dec 15 21:19:22.495 INFO [stdout] test src/lib.rs - (line 31) ... ok Dec 15 21:19:41.111 INFO [stdout] test src/pattern_matching/bndm.rs - pattern_matching::bndm (line 12) ... ok Dec 15 21:19:48.543 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder (line 9) ... ok Dec 15 21:19:51.366 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::build (line 142) ... ok Dec 15 21:19:51.391 INFO [stdout] test src/pattern_matching/kmp.rs - pattern_matching::kmp (line 16) ... ok Dec 15 21:19:53.401 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::ambig (line 63) ... ok Dec 15 21:19:53.834 INFO [stdout] test src/pattern_matching/horspool.rs - pattern_matching::horspool (line 32) ... ok Dec 15 21:19:57.443 INFO [stdout] test src/pattern_matching/bom.rs - pattern_matching::bom (line 12) ... ok Dec 15 21:20:04.071 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::text_wildcard (line 98) ... ok Dec 15 21:20:13.585 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 124) ... ok Dec 15 21:20:14.947 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 15) ... ok Dec 15 21:20:19.363 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 41) ... ok Dec 15 21:20:19.419 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 61) ... ok Dec 15 21:20:19.751 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 168) ... ok Dec 15 21:20:20.790 INFO [stdout] test src/pattern_matching/shift_and.rs - pattern_matching::shift_and (line 12) ... ok Dec 15 21:20:21.718 INFO [stdout] test src/pattern_matching/ukkonen.rs - pattern_matching::ukkonen (line 17) ... ok Dec 15 21:20:24.811 INFO [stdout] test src/seq_analysis/orf.rs - seq_analysis::orf (line 12) ... ok Dec 15 21:20:28.163 INFO [stdout] test src/stats/hmm.rs - stats::hmm (line 15) ... ok Dec 15 21:20:29.419 INFO [stdout] test src/stats/hmm.rs - stats::hmm (line 37) ... ok Dec 15 21:20:29.419 INFO [stdout] Dec 15 21:20:29.419 INFO [stdout] test result: ok. 58 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out Dec 15 21:20:29.419 INFO [stdout] Dec 15 21:20:29.459 INFO [stderr] su: No module specific data is present Dec 15 21:20:29.858 INFO running `"docker" "inspect" "6950bdd1f9d7a5057f2f68266ca24138a68cc36c8e59f5cd8401875560bd6a69"` Dec 15 21:20:29.985 INFO running `"docker" "rm" "-f" "6950bdd1f9d7a5057f2f68266ca24138a68cc36c8e59f5cd8401875560bd6a69"` Dec 15 21:20:30.074 INFO [stdout] 6950bdd1f9d7a5057f2f68266ca24138a68cc36c8e59f5cd8401875560bd6a69