Dec 07 22:42:16.074 INFO testing bio-0.24.0 against try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468 for pr-56514 Dec 07 22:42:16.074 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-0/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-0/pr-56514/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/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 +6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468-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 22:42:16.396 INFO [stdout] c4715b0102b40f02793562fb3c3e07bbcae55750aea2a8de691966aa63017320 Dec 07 22:42:16.408 INFO running `"docker" "start" "-a" "c4715b0102b40f02793562fb3c3e07bbcae55750aea2a8de691966aa63017320"` Dec 07 22:42:17.441 INFO [stderr] usermod: no changes Dec 07 22:42:17.740 INFO [stderr] Compiling feature-probe v0.1.1 Dec 07 22:42:17.740 INFO [stderr] Compiling bio v0.24.0 (/source) Dec 07 22:42:17.748 INFO [stderr] Compiling bio-types v0.4.0 Dec 07 22:42:19.256 INFO [stderr] Compiling bv v0.10.0 Dec 07 22:42:30.889 INFO [stderr] warning: unused import: `std::ops::Deref` Dec 07 22:42:30.889 INFO [stderr] --> src/data_structures/bwt.rs:15:5 Dec 07 22:42:30.889 INFO [stderr] | Dec 07 22:42:30.889 INFO [stderr] 15 | use std::ops::Deref; Dec 07 22:42:30.889 INFO [stderr] | ^^^^^^^^^^^^^^^ Dec 07 22:42:30.889 INFO [stderr] | Dec 07 22:42:30.889 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 07 22:42:30.889 INFO [stderr] Dec 07 22:42:32.844 INFO [stderr] warning: use of deprecated item 'ndarray::impl_methods::>::subview': renamed to `index_axis` Dec 07 22:42:32.845 INFO [stderr] --> src/stats/hmm.rs:266:22 Dec 07 22:42:32.845 INFO [stderr] | Dec 07 22:42:32.845 INFO [stderr] 266 | .subview(Axis(0), i - 1) Dec 07 22:42:32.845 INFO [stderr] | ^^^^^^^ Dec 07 22:42:32.852 INFO [stderr] | Dec 07 22:42:32.852 INFO [stderr] = note: #[warn(deprecated)] on by default Dec 07 22:42:32.852 INFO [stderr] Dec 07 22:42:39.416 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 21.94s Dec 07 22:42:39.422 INFO [stderr] su: No module specific data is present Dec 07 22:42:40.126 INFO running `"docker" "inspect" "c4715b0102b40f02793562fb3c3e07bbcae55750aea2a8de691966aa63017320"` Dec 07 22:42:40.304 INFO running `"docker" "rm" "-f" "c4715b0102b40f02793562fb3c3e07bbcae55750aea2a8de691966aa63017320"` Dec 07 22:42:40.648 INFO [stdout] c4715b0102b40f02793562fb3c3e07bbcae55750aea2a8de691966aa63017320 Dec 07 22:42:40.655 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-0/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-0/pr-56514/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/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 +6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468-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 22:42:41.110 INFO [stdout] 3af476c7c9b141af2ee5c8274de55f022b279b9cd7cdb9b1baf92c40016e49e9 Dec 07 22:42:41.116 INFO running `"docker" "start" "-a" "3af476c7c9b141af2ee5c8274de55f022b279b9cd7cdb9b1baf92c40016e49e9"` Dec 07 22:42:42.360 INFO [stderr] usermod: no changes Dec 07 22:42:42.497 INFO [stderr] Compiling bio v0.24.0 (/source) Dec 07 22:42:45.715 INFO [stderr] warning: unused import: `std::ops::Deref` Dec 07 22:42:45.715 INFO [stderr] --> src/data_structures/bwt.rs:15:5 Dec 07 22:42:45.715 INFO [stderr] | Dec 07 22:42:45.715 INFO [stderr] 15 | use std::ops::Deref; Dec 07 22:42:45.715 INFO [stderr] | ^^^^^^^^^^^^^^^ Dec 07 22:42:45.715 INFO [stderr] | Dec 07 22:42:45.715 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 07 22:42:45.715 INFO [stderr] Dec 07 22:42:49.009 INFO [stderr] warning: use of deprecated item 'ndarray::impl_methods::>::subview': renamed to `index_axis` Dec 07 22:42:49.009 INFO [stderr] --> src/stats/hmm.rs:266:22 Dec 07 22:42:49.009 INFO [stderr] | Dec 07 22:42:49.009 INFO [stderr] 266 | .subview(Axis(0), i - 1) Dec 07 22:42:49.009 INFO [stderr] | ^^^^^^^ Dec 07 22:42:49.009 INFO [stderr] | Dec 07 22:42:49.009 INFO [stderr] = note: #[warn(deprecated)] on by default Dec 07 22:42:49.016 INFO [stderr] Dec 07 22:43:06.688 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 24.29s Dec 07 22:43:06.695 INFO [stderr] su: No module specific data is present Dec 07 22:43:07.610 INFO running `"docker" "inspect" "3af476c7c9b141af2ee5c8274de55f022b279b9cd7cdb9b1baf92c40016e49e9"` Dec 07 22:43:07.918 INFO running `"docker" "rm" "-f" "3af476c7c9b141af2ee5c8274de55f022b279b9cd7cdb9b1baf92c40016e49e9"` Dec 07 22:43:08.227 INFO [stdout] 3af476c7c9b141af2ee5c8274de55f022b279b9cd7cdb9b1baf92c40016e49e9 Dec 07 22:43:08.236 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-0/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-0/pr-56514/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/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 +6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468-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 22:43:08.645 INFO [stdout] 33006b4583a3147007c812352d7e2d4653ab882542466a9d9549657243d96725 Dec 07 22:43:08.647 INFO running `"docker" "start" "-a" "33006b4583a3147007c812352d7e2d4653ab882542466a9d9549657243d96725"` Dec 07 22:43:10.404 INFO [stderr] usermod: no changes Dec 07 22:43:10.568 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 0.14s Dec 07 22:43:10.580 INFO [stderr] Running /target/debug/deps/bio-302c4aa0e0944401 Dec 07 22:43:10.580 INFO [stdout] Dec 07 22:43:10.580 INFO [stdout] running 245 tests Dec 07 22:43:10.592 INFO [stdout] test alignment::pairwise::banded::banded::test_band_add_kmer ... ok Dec 07 22:43:10.592 INFO [stdout] test alignment::pairwise::banded::banded::test_band_add_entry ... ok Dec 07 22:43:10.592 INFO [stdout] test alignment::pairwise::banded::banded::test_aligner_new ... ok Dec 07 22:43:10.604 INFO [stdout] test alignment::distance::tests::test_levenshtein_dist ... ok Dec 07 22:43:10.604 INFO [stdout] test alignment::distance::tests::test_hamming_dist_good ... ok Dec 07 22:43:10.604 INFO [stdout] test alignment::pairwise::banded::banded::test_blosum62 ... ok Dec 07 22:43:10.609 INFO [stdout] test alignment::pairwise::banded::banded::test_global ... ok Dec 07 22:43:10.609 INFO [stdout] test alignment::pairwise::banded::banded::test_global_affine_ins2 ... ok Dec 07 22:43:10.609 INFO [stdout] test alignment::pairwise::banded::banded::test_global_right_del ... ok Dec 07 22:43:10.609 INFO [stdout] test alignment::pairwise::banded::banded::test_insert_in_between_semiglobal ... ok Dec 07 22:43:10.609 INFO [stdout] test alignment::pairwise::banded::banded::test_insert_only_semiglobal ... ok Dec 07 22:43:10.612 INFO [stdout] test alignment::pairwise::banded::banded::test_global_affine_ins ... ok Dec 07 22:43:10.624 INFO [stdout] test alignment::pairwise::banded::banded::test_issue11 ... ok Dec 07 22:43:10.640 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_1 ... ok Dec 07 22:43:10.655 INFO [stdout] test alignment::pairwise::banded::banded::test_deletion ... ok Dec 07 22:43:10.672 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_2 ... ok Dec 07 22:43:10.672 INFO [stdout] test alignment::pairwise::banded::banded::test_left_aligned_del ... ok Dec 07 22:43:10.672 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_3 ... ok Dec 07 22:43:10.677 INFO [stdout] test alignment::pairwise::banded::banded::test_insertion ... ok Dec 07 22:43:10.677 INFO [stdout] test alignment::pairwise::banded::banded::test_left_aligned_ins ... ok Dec 07 22:43:10.677 INFO [stdout] test alignment::pairwise::banded::banded::test_local ... ok Dec 07 22:43:10.677 INFO [stdout] test alignment::pairwise::banded::banded::test_local_affine_ins2 ... ok Dec 07 22:43:10.684 INFO [stdout] test alignment::pairwise::banded::banded::test_longer_string_all_operations ... ok Dec 07 22:43:10.696 INFO [stdout] test alignment::pairwise::banded::banded::test_local_empty ... ok Dec 07 22:43:10.696 INFO [stdout] test alignment::pairwise::banded::banded::test_band_ends_inside ... ok Dec 07 22:43:10.700 INFO [stdout] test alignment::pairwise::banded::banded::test_band_starts_inside ... ok Dec 07 22:43:10.772 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs1 ... ok Dec 07 22:43:10.776 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs3 ... ok Dec 07 22:43:10.776 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal ... ok Dec 07 22:43:10.784 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal_gap_open_lt_mismatch ... ok Dec 07 22:43:10.784 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal_simple ... ok Dec 07 22:43:10.792 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs2 ... ok Dec 07 22:43:10.796 INFO [stdout] test alignment::pairwise::banded::banded::test_band_is_fully_inside ... ok Dec 07 22:43:10.820 INFO [stdout] test alignment::pairwise::banded::banded::test_xclip_prefix_custom ... ok Dec 07 22:43:10.824 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs4 ... ok Dec 07 22:43:10.824 INFO [stdout] test alignment::pairwise::banded::banded::test_yclip_prefix_custom ... ok Dec 07 22:43:10.824 INFO [stdout] test alignment::pairwise::banded::banded::test_xclip_suffix_custom ... ok Dec 07 22:43:10.836 INFO [stdout] test alignment::pairwise::banded::banded::test_yclip_suffix_custom ... ok Dec 07 22:43:10.836 INFO [stdout] test alignment::pairwise::tests::test_aligner_new ... ok Dec 07 22:43:10.836 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs5 ... ok Dec 07 22:43:10.836 INFO [stdout] test alignment::pairwise::tests::test_blosum62 ... ok Dec 07 22:43:10.852 INFO [stdout] test alignment::pairwise::tests::test_global_affine_ins ... ok Dec 07 22:43:10.852 INFO [stdout] test alignment::pairwise::tests::test_insert_in_between_semiglobal ... ok Dec 07 22:43:10.852 INFO [stdout] test alignment::pairwise::tests::test_global ... ok Dec 07 22:43:10.860 INFO [stdout] test alignment::pairwise::tests::test_insert_only_semiglobal ... ok Dec 07 22:43:10.860 INFO [stdout] test alignment::pairwise::tests::test_issue11 ... ok Dec 07 22:43:10.860 INFO [stdout] test alignment::pairwise::tests::test_issue12_1 ... ok Dec 07 22:43:10.868 INFO [stdout] test alignment::pairwise::tests::test_issue12_2 ... ok Dec 07 22:43:10.868 INFO [stdout] test alignment::pairwise::tests::test_issue12_3 ... ok Dec 07 22:43:10.868 INFO [stdout] test alignment::pairwise::tests::test_global_affine_ins2 ... ok Dec 07 22:43:10.868 INFO [stdout] test alignment::pairwise::tests::test_global_right_del ... ok Dec 07 22:43:10.868 INFO [stdout] test alignment::pairwise::tests::test_left_aligned_del ... ok Dec 07 22:43:10.868 INFO [stdout] test alignment::pairwise::tests::test_left_aligned_ins ... ok Dec 07 22:43:10.868 INFO [stdout] test alignment::pairwise::tests::test_local ... ok Dec 07 22:43:10.868 INFO [stdout] test alignment::pairwise::tests::test_local_affine_ins2 ... ok Dec 07 22:43:10.868 INFO [stdout] test alignment::pairwise::tests::test_semiglobal_gap_open_lt_mismatch ... ok Dec 07 22:43:10.868 INFO [stdout] test alignment::pairwise::tests::test_semiglobal ... ok Dec 07 22:43:10.868 INFO [stdout] test alignment::pairwise::tests::test_scoring_from_scores ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::pairwise::tests::test_longer_string_all_operations ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::pairwise::tests::test_xclip_prefix_custom ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::pairwise::tests::test_semiglobal_simple ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::pairwise::tests::test_xclip_suffix_custom ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::sparse::sparse_alignment::test_expanded_matches ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::pairwise::tests::test_yclip_suffix_custom ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::pairwise::tests::traceback_cell ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::pairwise::tests::test_yclip_prefix_custom ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::sparse::sparse_alignment::test_find_kmer_matches ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp0 ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp1 ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp2 ... ok Dec 07 22:43:10.872 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp ... ok Dec 07 22:43:10.881 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp_same ... ok Dec 07 22:43:10.881 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdpkpp_same ... ok Dec 07 22:43:10.881 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp1 ... ok Dec 07 22:43:10.888 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp2 ... ok Dec 07 22:43:10.888 INFO [stdout] test alphabets::protein::tests::is_no_word ... ok Dec 07 22:43:10.896 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp_tandem_repeat ... ok Dec 07 22:43:10.896 INFO [stdout] test alphabets::protein::tests::number_is_no_word ... ok Dec 07 22:43:10.904 INFO [stdout] test alphabets::rna::tests::is_no_word ... ok Dec 07 22:43:10.904 INFO [stdout] test alphabets::rna::tests::is_word ... ok Dec 07 22:43:10.904 INFO [stdout] test alphabets::protein::tests::is_word ... ok Dec 07 22:43:10.904 INFO [stdout] test alphabets::protein::tests::symbol_is_no_word ... ok Dec 07 22:43:10.908 INFO [stdout] test alphabets::rna::tests::symbol_is_no_word ... ok Dec 07 22:43:10.908 INFO [stdout] test data_structures::annot_map::tests::lookup ... ok Dec 07 22:43:10.908 INFO [stdout] test data_structures::annot_map::tests::overlaps ... ok Dec 07 22:43:10.908 INFO [stdout] test data_structures::bit_tree::test_bit_tree::test_bit_tree ... ok Dec 07 22:43:10.908 INFO [stdout] test data_structures::bitenc::tests::test_bitenc ... ok Dec 07 22:43:10.914 INFO [stdout] test alphabets::rna::tests::test_reverse_complement ... ok Dec 07 22:43:10.914 INFO [stdout] test alphabets::rna::tests::number_is_no_word ... ok Dec 07 22:43:10.941 INFO [stdout] test alignment::pairwise::banded::banded::test_substitutions ... ok Dec 07 22:43:10.941 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdpkpp_tandem_repeat ... ok Dec 07 22:43:10.944 INFO [stdout] test data_structures::bitenc::tests::test_push_values ... ok Dec 07 22:43:10.944 INFO [stdout] test data_structures::bwt::tests::test_bwtfind ... ok Dec 07 22:43:10.944 INFO [stdout] test data_structures::bitenc::tests::test_issue29 ... ok Dec 07 22:43:10.948 INFO [stdout] test data_structures::fmindex::tests::test_fmindex ... ok Dec 07 22:43:10.948 INFO [stdout] test data_structures::bwt::tests::test_invert_bwt ... ok Dec 07 22:43:10.948 INFO [stdout] test data_structures::bwt::tests::test_occ ... ok Dec 07 22:43:10.948 INFO [stdout] test data_structures::fmindex::tests::test_init_interval ... ok Dec 07 22:43:10.956 INFO [stdout] test data_structures::interval_tree::tests::from_iterator ... ok Dec 07 22:43:10.956 INFO [stdout] test data_structures::interval_tree::tests::iter_mut ... ok Dec 07 22:43:10.988 INFO [stdout] test data_structures::fmindex::tests::test_smems ... ok Dec 07 22:43:11.016 INFO [stdout] test alignment::pairwise::banded::banded::test_same ... ok Dec 07 22:43:11.016 INFO [stdout] test data_structures::interval_tree::tests::test_insertion_and_intersection ... ok Dec 07 22:43:11.016 INFO [stdout] test data_structures::interval_tree::tests::zero_width_ranges ... ok Dec 07 22:43:11.016 INFO [stdout] test data_structures::qgram_index::tests::test_matches ... ok Dec 07 22:43:11.016 INFO [stdout] test data_structures::qgram_index::tests::test_exact_matches ... ok Dec 07 22:43:11.060 INFO [stdout] test alignment::distance::tests::test_hamming_dist_bad ... ok Dec 07 22:43:11.060 INFO [stdout] test data_structures::rank_select::tests::test_select ... ok Dec 07 22:43:11.060 INFO [stdout] test data_structures::rank_select::tests::test_single_select ... ok Dec 07 22:43:11.060 INFO [stdout] test data_structures::suffix_array::tests::test_buckets ... ok Dec 07 22:43:11.076 INFO [stdout] test data_structures::qgram_index::tests::test_exact_matches_self ... ok Dec 07 22:43:11.076 INFO [stdout] test data_structures::rank_select::tests::test_rank_select ... ok Dec 07 22:43:11.076 INFO [stdout] test data_structures::qgram_index::tests::test_qgram_matches ... ok Dec 07 22:43:11.076 INFO [stdout] test data_structures::suffix_array::tests::test_lms_pos ... ok Dec 07 22:43:11.076 INFO [stdout] test data_structures::suffix_array::tests::test_issue10_2 ... ok Dec 07 22:43:11.076 INFO [stdout] test data_structures::suffix_array::tests::test_pos ... ok Dec 07 22:43:11.076 INFO [stdout] test data_structures::suffix_array::tests::test_handles_sentinels_properly ... ok Dec 07 22:43:11.076 INFO [stdout] test data_structures::suffix_array::tests::test_issue10_1 ... ok Dec 07 22:43:11.076 INFO [stdout] test data_structures::suffix_array::tests::test_pos_types ... ok Dec 07 22:43:11.076 INFO [stdout] test io::bed::tests::test_reader ... ok Dec 07 22:43:11.076 INFO [stdout] test io::bed::tests::spliced_to_bed ... ok Dec 07 22:43:11.088 INFO [stdout] test io::bed::tests::test_writer ... ok Dec 07 22:43:11.088 INFO [stdout] test io::fasta::tests::test_indexed_reader ... ok Dec 07 22:43:11.090 INFO [stdout] test io::fasta::tests::test_indexed_reader_all ... ok Dec 07 22:43:11.090 INFO [stdout] test io::fasta::tests::test_indexed_reader_bad_reader ... ok Dec 07 22:43:11.098 INFO [stdout] test io::fasta::tests::test_indexed_reader_by_rid_all ... ok Dec 07 22:43:11.098 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf ... ok Dec 07 22:43:11.098 INFO [stdout] test io::fasta::tests::test_index_sequences ... ok Dec 07 22:43:11.098 INFO [stdout] test data_structures::suffix_array::tests::test_sorts_lexically ... ok Dec 07 22:43:11.100 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf_by_rid_all ... ok Dec 07 22:43:11.106 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf_all ... ok Dec 07 22:43:11.106 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_all ... ok Dec 07 22:43:11.106 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_by_rid_all ... ok Dec 07 22:43:11.106 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf_all ... ok Dec 07 22:43:11.126 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf_by_rid_all ... ok Dec 07 22:43:11.126 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter ... ok Dec 07 22:43:11.126 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf ... ok Dec 07 22:43:11.126 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_read_fails ... ok Dec 07 22:43:11.126 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_fetch_read_fails ... ok Dec 07 22:43:11.126 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_fetch_read_iter_fails ... ok Dec 07 22:43:11.126 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_trailing_lf ... ok Dec 07 22:43:11.126 INFO [stdout] test io::fasta::tests::test_indexed_reader_read_read_fails ... ok Dec 07 22:43:11.129 INFO [stdout] test io::fasta::tests::test_indexed_reader_read_seek_fails ... ok Dec 07 22:43:11.129 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_seek_fails ... ok Dec 07 22:43:11.140 INFO [stdout] test io::fasta::tests::test_indexed_reader_reused_buffer ... ok Dec 07 22:43:11.140 INFO [stdout] test io::fasta::tests::test_reader_no_id ... ok Dec 07 22:43:11.140 INFO [stdout] test io::fasta::tests::test_reader ... ok Dec 07 22:43:11.140 INFO [stdout] test io::fasta::tests::test_reader_read_fails ... ok Dec 07 22:43:11.140 INFO [stdout] test io::fasta::tests::test_reader_non_ascii_sequence ... ok Dec 07 22:43:11.140 INFO [stdout] test io::fasta::tests::test_reader_wrong_header ... ok Dec 07 22:43:11.140 INFO [stdout] test io::fasta::tests::test_record_with_attrs ... ok Dec 07 22:43:11.140 INFO [stdout] test io::fasta::tests::test_writer ... ok Dec 07 22:43:11.140 INFO [stdout] test io::fasta::tests::test_reader_read_fails_iter ... ok Dec 07 22:43:11.140 INFO [stdout] test io::fastq::tests::test_reader ... ok Dec 07 22:43:11.140 INFO [stdout] test io::fastq::tests::test_writer ... ok Dec 07 22:43:11.149 INFO [stdout] test io::gff::tests::test_convert_gtf2_to_gff3 ... ok Dec 07 22:43:11.164 INFO [stdout] test io::fastq::tests::test_record_with_attrs ... ok Dec 07 22:43:11.164 INFO [stdout] test data_structures::fmindex::tests::test_issue39 ... ok Dec 07 22:43:11.176 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_size_hint ... ok Dec 07 22:43:11.188 INFO [stdout] test io::gff::tests::test_reader_gtf2_2 ... ok Dec 07 22:43:11.208 INFO [stdout] test io::gff::tests::test_reader_gff3 ... ok Dec 07 22:43:11.244 INFO [stdout] test io::gff::tests::test_reader_gtf2_dup_attr_keys ... ok Dec 07 22:43:11.244 INFO [stdout] test io::gff::tests::test_reader_gtf2 ... ok Dec 07 22:43:11.244 INFO [stdout] test io::gff::tests::test_writer_gtf2 ... ok Dec 07 22:43:11.252 INFO [stdout] test pattern_matching::horspool::tests::test_find_all ... ok Dec 07 22:43:11.252 INFO [stdout] test pattern_matching::horspool::tests::test_shift ... ok Dec 07 22:43:11.252 INFO [stdout] test pattern_matching::bom::tests::test_delta ... ok Dec 07 22:43:11.252 INFO [stdout] test pattern_matching::bndm::tests::test_find_all ... ok Dec 07 22:43:11.252 INFO [stdout] test pattern_matching::bom::tests::test_find_all ... ok Dec 07 22:43:11.252 INFO [stdout] test pattern_matching::kmp::tests::test_find_all ... ok Dec 07 22:43:11.260 INFO [stdout] test pattern_matching::kmp::tests::test_delta ... ok Dec 07 22:43:11.260 INFO [stdout] test io::gff::tests::test_writer_gff3 ... ok Dec 07 22:43:11.276 INFO [stdout] test data_structures::interval_tree::tests::test_insertion_and_intersection_2 ... ok Dec 07 22:43:11.276 INFO [stdout] test pattern_matching::myers::tests::test_find_all_end ... ok Dec 07 22:43:11.276 INFO [stdout] test pattern_matching::myers::tests::test_find_best_end ... ok Dec 07 22:43:11.276 INFO [stdout] test pattern_matching::myers::tests::test_full_position ... ok Dec 07 22:43:11.276 INFO [stdout] test pattern_matching::kmp::tests::test_lps ... ok Dec 07 22:43:11.284 INFO [stdout] test pattern_matching::myers::tests::test_large_dist ... ok Dec 07 22:43:11.284 INFO [stdout] test pattern_matching::myers::tests::test_long_shorter ... ok Dec 07 22:43:11.284 INFO [stdout] test pattern_matching::myers::tests::test_path_at ... ok Dec 07 22:43:11.284 INFO [stdout] test pattern_matching::myers::tests::test_longest_possible ... ok Dec 07 22:43:11.284 INFO [stdout] test pattern_matching::myers::tests::test_alignment ... ok Dec 07 22:43:11.284 INFO [stdout] test pattern_matching::kmp::tests::test_find_all_at_start ... ok Dec 07 22:43:11.284 INFO [stdout] test pattern_matching::myers::tests::test_distance ... ok Dec 07 22:43:11.284 INFO [stdout] test pattern_matching::myers::tests::test_ambig ... ok Dec 07 22:43:11.284 INFO [stdout] test pattern_matching::myers::tests::test_shorter ... ok Dec 07 22:43:11.284 INFO [stdout] test pattern_matching::myers::tests::test_position_cmp ... ok Dec 07 22:43:11.292 INFO [stdout] test pattern_matching::myers::tests::test_traceback_path ... ok Dec 07 22:43:11.292 INFO [stdout] test pattern_matching::myers::tests::test_traceback_path2 ... ok Dec 07 22:43:11.292 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_inconsist_err ... ok Dec 07 22:43:11.292 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::find_motif ... ok Dec 07 22:43:11.292 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::simple_pssm ... ok Dec 07 22:43:11.292 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_info_content ... ok Dec 07 22:43:11.304 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_mono_err ... ok Dec 07 22:43:11.304 INFO [stdout] test pattern_matching::myers::tests::test_pattern_too_long ... ok Dec 07 22:43:11.308 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_scoring ... ok Dec 07 22:43:11.309 INFO [stdout] test pattern_matching::shift_and::tests::test_find_all ... ok Dec 07 22:43:11.309 INFO [stdout] test pattern_matching::ukkonen::tests::test_find_all_end ... ok Dec 07 22:43:11.309 INFO [stdout] test pattern_matching::ukkonen::tests::test_find_start ... ok Dec 07 22:43:11.309 INFO [stdout] test scores::blosum62::tests::test_blosum62 ... ok Dec 07 22:43:11.309 INFO [stdout] test scores::pam120::tests::test_pam120 ... ok Dec 07 22:43:11.309 INFO [stdout] test scores::pam200::tests::test_pam200 ... ok Dec 07 22:43:11.309 INFO [stdout] test scores::pam250::tests::test_pam250 ... ok Dec 07 22:43:11.309 INFO [stdout] test scores::pam40::tests::test_pam40 ... ok Dec 07 22:43:11.309 INFO [stdout] test seq_analysis::orf::tests::test_orf ... ok Dec 07 22:43:11.309 INFO [stdout] test stats::bayesian::tests::test_expected_fdr ... ok Dec 07 22:43:11.309 INFO [stdout] test stats::combinatorics::tests::test_comb ... ok Dec 07 22:43:11.309 INFO [stdout] test stats::combinatorics::tests::test_comb_scaled ... ok Dec 07 22:43:11.309 INFO [stdout] test stats::hmm::tests::test_discrete_backward_toy_example ... ok Dec 07 22:43:11.309 INFO [stdout] test stats::hmm::tests::test_discrete_forward_toy_example ... ok Dec 07 22:43:11.309 INFO [stdout] test stats::hmm::tests::test_discrete_viterbi_toy_example ... ok Dec 07 22:43:11.309 INFO [stdout] test stats::hmm::tests::test_gaussian_backward_simple_example ... ok Dec 07 22:43:11.320 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_mono_err ... ok Dec 07 22:43:11.320 INFO [stdout] test stats::hmm::tests::test_gaussian_forward_equals_backward_simple_example ... ok Dec 07 22:43:11.320 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_info_content ... ok Dec 07 22:43:11.320 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_inconsist_err ... ok Dec 07 22:43:11.320 INFO [stdout] test pattern_matching::myers::tests::test_pattern_too_long_builder ... ok Dec 07 22:43:11.320 INFO [stdout] test stats::hmm::tests::test_gaussian_forward_simple_example ... ok Dec 07 22:43:11.320 INFO [stdout] test stats::pairhmm::tests::test_mismatch ... ok Dec 07 22:43:11.320 INFO [stdout] test stats::pairhmm::tests::test_same ... ok Dec 07 22:43:11.320 INFO [stdout] test stats::pairhmm::tests::test_insertion ... ok Dec 07 22:43:11.328 INFO [stdout] test stats::probs::cdf::test::test_cdf ... ok Dec 07 22:43:11.328 INFO [stdout] test stats::probs::tests::test_cap_numerical_overshoot ... ok Dec 07 22:43:11.332 INFO [stdout] test stats::probs::tests::test_cumsum ... ok Dec 07 22:43:11.332 INFO [stdout] test stats::hmm::tests::test_gaussian_viterbi_simple_example ... ok Dec 07 22:43:11.340 INFO [stdout] test stats::pairhmm::tests::test_deletion ... ok Dec 07 22:43:11.356 INFO [stdout] test stats::probs::tests::test_one_minus ... ok Dec 07 22:43:11.356 INFO [stdout] test stats::probs::tests::test_empty_sum ... ok Dec 07 22:43:11.356 INFO [stdout] test stats::probs::tests::test_simpsons_integrate ... ok Dec 07 22:43:11.364 INFO [stdout] test stats::probs::tests::test_cap_numerical_overshoot_panic ... ok Dec 07 22:43:11.364 INFO [stdout] test stats::probs::tests::test_sub ... ok Dec 07 22:43:11.364 INFO [stdout] test stats::probs::tests::test_zero ... ok Dec 07 22:43:11.364 INFO [stdout] test stats::probs::tests::test_trapezoidal_integrate ... ok Dec 07 22:43:11.364 INFO [stdout] test stats::probs::tests::test_sum_one_zero ... ok Dec 07 22:43:11.368 INFO [stdout] test stats::probs::tests::test_sum ... ok Dec 07 22:43:11.372 INFO [stdout] test utils::fastexp::tests::test_fastexp ... ok Dec 07 22:43:11.375 INFO [stdout] test stats::pairhmm::tests::test_large ... ok Dec 07 22:43:11.384 INFO [stdout] test utils::interval::tests::range_interval_conversions ... ok Dec 07 22:43:11.392 INFO [stdout] test utils::text::tests::test_print_sequence ... ok Dec 07 22:43:11.408 INFO [stdout] test utils::tests::test_prescan ... ok Dec 07 22:43:11.408 INFO [stdout] test utils::tests::test_scan ... ok Dec 07 22:43:11.424 INFO [stdout] test utils::interval::tests::negative_width_range ... ok Dec 07 22:43:11.443 INFO [stdout] test alignment::pairwise::banded::banded::test_big ... ok Dec 07 22:43:11.483 INFO [stdout] test data_structures::interpolation_table::tests::test_interpolation_table ... ok Dec 07 22:43:11.564 INFO [stdout] test stats::hmm::tests::test_discrete_forward_equals_backward_toy_example ... ok Dec 07 22:43:11.564 INFO [stderr] Doc-tests bio Dec 07 22:43:11.564 INFO [stdout] Dec 07 22:43:11.564 INFO [stdout] test result: ok. 245 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out Dec 07 22:43:11.564 INFO [stdout] Dec 07 22:43:15.801 INFO [stdout] Dec 07 22:43:15.801 INFO [stdout] running 58 tests Dec 07 22:43:32.924 INFO [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise (line 13) ... ok Dec 07 22:43:34.008 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::PHREDProb (line 46) ... ok Dec 07 22:43:35.160 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::Prob (line 46) ... ok Dec 07 22:43:36.108 INFO [stdout] test src/alignment/distance.rs - alignment::distance::hamming (line 16) ... ok Dec 07 22:43:40.220 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::LogProb (line 50) ... ok Dec 07 22:43:42.728 INFO [stdout] test src/alignment/distance.rs - alignment::distance::levenshtein (line 48) ... ok Dec 07 22:43:43.478 INFO [stdout] test src/alignment/sparse.rs - alignment::sparse (line 18) ... ok Dec 07 22:43:50.292 INFO [stdout] test src/alignment/pairwise/banded.rs - alignment::pairwise::banded (line 20) ... ok Dec 07 22:44:11.304 INFO [stdout] test src/alphabets/dna.rs - alphabets::dna (line 10) ... ok Dec 07 22:44:13.183 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::insert_at (line 58) ... ok Dec 07 22:44:14.470 INFO [stdout] test src/alphabets/protein.rs - alphabets::protein (line 10) ... ok Dec 07 22:44:17.793 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::find (line 92) ... ok Dec 07 22:44:18.957 INFO [stdout] test src/alphabets/mod.rs - alphabets (line 10) ... ok Dec 07 22:44:20.959 INFO [stdout] test src/alphabets/rna.rs - alphabets::rna (line 10) ... ok Dec 07 22:44:22.920 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::new (line 39) ... ok Dec 07 22:44:35.073 INFO [stdout] test src/data_structures/bit_tree.rs - data_structures::bit_tree (line 12) ... ok Dec 07 22:44:57.040 INFO [stdout] test src/data_structures/bitenc.rs - data_structures::bitenc (line 11) ... ok Dec 07 22:44:57.052 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex (line 32) ... ok Dec 07 22:44:58.300 INFO [stdout] test src/data_structures/bwt.rs - data_structures::bwt::bwt (line 33) ... ok Dec 07 22:44:58.936 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex (line 12) ... ok Dec 07 22:45:01.297 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex::FMDIndex::smems (line 260) ... ok Dec 07 22:45:04.992 INFO [stdout] test src/data_structures/interval_tree.rs - data_structures::interval_tree (line 14) ... ok Dec 07 22:45:05.278 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex::FMIndexable::backward_search (line 96) ... ok Dec 07 22:45:17.804 INFO [stdout] test src/data_structures/qgram_index.rs - data_structures::qgram_index (line 10) ... ok Dec 07 22:45:22.548 INFO [stdout] test src/data_structures/rank_select.rs - data_structures::rank_select (line 11) ... ok Dec 07 22:45:31.552 INFO [stdout] test src/data_structures/smallints.rs - data_structures::smallints (line 13) ... ok Dec 07 22:45:35.140 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::lcp (line 239) ... ok Dec 07 22:45:39.480 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::suffix_array (line 198) ... ok Dec 07 22:45:40.560 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::shortest_unique_substrings (line 304) ... ok Dec 07 22:45:44.556 INFO [stdout] test src/io/bed.rs - io::bed::Record (line 314) ... ok Dec 07 22:45:47.220 INFO [stdout] test src/io/bed.rs - io::bed (line 10) ... ok Dec 07 22:46:00.136 INFO [stdout] test src/io/bed.rs - io::bed::annot::contig::Contig::from (line 237) ... ok Dec 07 22:46:01.840 INFO [stdout] test src/io/fasta.rs - io::fasta (line 10) ... ok Dec 07 22:46:12.052 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::new (line 49) ... ok Dec 07 22:46:17.116 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::read (line 69) ... ok Dec 07 22:46:20.996 INFO [stdout] test src/io/fastq.rs - io::fastq (line 10) ... ok Dec 07 22:46:23.624 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::records (line 127) ... ok Dec 07 22:46:24.784 INFO [stdout] test src/io/gff.rs - io::gff (line 14) ... ok Dec 07 22:46:28.364 INFO [stdout] test src/lib.rs - (line 31) ... ok Dec 07 22:46:42.344 INFO [stdout] test src/pattern_matching/bndm.rs - pattern_matching::bndm (line 12) ... ok Dec 07 22:46:42.477 INFO [stdout] test src/lib.rs - (line 54) ... ok Dec 07 22:46:48.864 INFO [stdout] test src/pattern_matching/bom.rs - pattern_matching::bom (line 12) ... ok Dec 07 22:46:54.724 INFO [stdout] test src/pattern_matching/horspool.rs - pattern_matching::horspool (line 32) ... ok Dec 07 22:46:57.452 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder (line 9) ... ok Dec 07 22:46:57.736 INFO [stdout] test src/pattern_matching/kmp.rs - pattern_matching::kmp (line 16) ... ok Dec 07 22:47:01.764 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::ambig (line 63) ... ok Dec 07 22:47:03.632 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::build (line 142) ... ok Dec 07 22:47:20.356 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::text_wildcard (line 98) ... ok Dec 07 22:47:25.310 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 124) ... ok Dec 07 22:47:25.812 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 15) ... ok Dec 07 22:47:31.148 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 168) ... ok Dec 07 22:47:36.744 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 61) ... ok Dec 07 22:47:37.607 INFO [stdout] test src/pattern_matching/ukkonen.rs - pattern_matching::ukkonen (line 17) ... ok Dec 07 22:47:38.965 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 41) ... ok Dec 07 22:47:39.232 INFO [stdout] test src/pattern_matching/shift_and.rs - pattern_matching::shift_and (line 12) ... ok Dec 07 22:47:43.172 INFO [stdout] test src/seq_analysis/orf.rs - seq_analysis::orf (line 12) ... ok Dec 07 22:47:43.264 INFO [stdout] test src/stats/hmm.rs - stats::hmm (line 15) ... ok Dec 07 22:47:45.180 INFO [stdout] test src/stats/hmm.rs - stats::hmm (line 37) ... ok Dec 07 22:47:45.180 INFO [stdout] Dec 07 22:47:45.180 INFO [stdout] test result: ok. 58 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out Dec 07 22:47:45.180 INFO [stdout] Dec 07 22:47:45.228 INFO [stderr] su: No module specific data is present Dec 07 22:47:45.693 INFO running `"docker" "inspect" "33006b4583a3147007c812352d7e2d4653ab882542466a9d9549657243d96725"` Dec 07 22:47:46.100 INFO running `"docker" "rm" "-f" "33006b4583a3147007c812352d7e2d4653ab882542466a9d9549657243d96725"` Dec 07 22:47:46.290 INFO [stdout] 33006b4583a3147007c812352d7e2d4653ab882542466a9d9549657243d96725