[INFO] fetching crate dada2-rs 0.2.0...
[INFO] testing dada2-rs-0.2.0 against 1.99.0-beta.8+cargoflags=--release for beta-release-1.100-2
[INFO] extracting crate dada2-rs 0.2.0 into /workspace/builds/worker-7-tc1/source
[INFO] started tweaking crates.io crate dada2-rs 0.2.0
[INFO] removed 0 missing tests
[INFO] finished tweaking crates.io crate dada2-rs 0.2.0
[INFO] tweaked toml for crates.io crate dada2-rs 0.2.0 written to /workspace/builds/worker-7-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate dada2-rs 0.2.0 on toolchain 1.99.0-beta.8
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.99.0-beta.8" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate dada2-rs 0.2.0 already has a lockfile, it will not be regenerated
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.99.0-beta.8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded matrixmultiply v0.3.10
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[INFO] [stderr]   Downloaded statrs v0.18.0
[INFO] [stderr]   Downloaded nalgebra v0.33.3
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:77db811e55d90add9212f6832c23229e3de5f1c1f9905e8cb07319ea15df73ac" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1
[INFO] running `Command { std: "docker" "start" "71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "build" "--frozen" "--message-format=json" "--release", kill_on_drop: false }`
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[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling crc32fast v1.5.0
[INFO] [stderr]    Compiling simd-adler32 v0.3.9
[INFO] [stderr]    Compiling bytemuck v1.25.0
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[INFO] [stderr]    Compiling bstr v1.12.1
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[INFO] [stderr]    Compiling rayon-core v1.13.0
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[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling clap_derive v4.6.0
[INFO] [stderr]    Compiling dada2-rs v0.2.0 (/opt/rustwide/workdir)
[INFO] [stderr]    Compiling either v1.15.0
[INFO] [stderr]    Compiling sha1 v0.10.6
[INFO] [stderr]    Compiling rayon v1.11.0
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[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 2m 20s
[INFO] running `Command { std: "docker" "inspect" "71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen" "--no-run" "--message-format=json" "--release", kill_on_drop: false }`
[INFO] [stderr]    Compiling dada2-rs v0.2.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: value assigned to `i0` is never read
[INFO] [stdout]     --> src/nwalign.rs:1941:22
[INFO] [stdout]      |
[INFO] [stdout] 1941 |         let mut i0 = false; // was previous al0[k] a gap?
[INFO] [stdout]      |                      ^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 1952 |                 i0 = false;
[INFO] [stdout]      |                 ---------- `i0` is overwritten here before the previous value is read
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `i0` is never read
[INFO] [stdout]     --> src/nwalign.rs:1952:17
[INFO] [stdout]      |
[INFO] [stdout] 1952 |                 i0 = false;
[INFO] [stdout]      |                 ^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 1967 |                 i0 = true;
[INFO] [stdout]      |                 --------- `i0` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `i0` is never read
[INFO] [stdout]     --> src/nwalign.rs:1967:17
[INFO] [stdout]      |
[INFO] [stdout] 1958 |                 i0 = false;
[INFO] [stdout]      |                 ---------- `i0` is overwritten here before the previous value is read
[INFO] [stdout] ...
[INFO] [stdout] 1967 |                 i0 = true;
[INFO] [stdout]      |                 ^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]     --> src/nwalign.rs:2566:13
[INFO] [stdout]      |
[INFO] [stdout] 2566 |         let mut rng = |st: &mut u64, m: usize| {
[INFO] [stdout]      |             ----^^^
[INFO] [stdout]      |             |
[INFO] [stdout]      |             help: remove this `mut`
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 1m 27s
[INFO] running `Command { std: "docker" "inspect" "71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen" "--release", kill_on_drop: false }`
[INFO] [stderr]    Compiling dada2-rs v0.2.0 (/opt/rustwide/workdir)
[INFO] [stderr] warning: value assigned to `i0` is never read
[INFO] [stderr]     --> src/nwalign.rs:1941:22
[INFO] [stderr]      |
[INFO] [stderr] 1941 |         let mut i0 = false; // was previous al0[k] a gap?
[INFO] [stderr]      |                      ^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 1952 |                 i0 = false;
[INFO] [stderr]      |                 ---------- `i0` is overwritten here before the previous value is read
[INFO] [stderr]      |
[INFO] [stderr]      = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `i0` is never read
[INFO] [stderr]     --> src/nwalign.rs:1952:17
[INFO] [stderr]      |
[INFO] [stderr] 1952 |                 i0 = false;
[INFO] [stderr]      |                 ^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 1967 |                 i0 = true;
[INFO] [stderr]      |                 --------- `i0` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `i0` is never read
[INFO] [stderr]     --> src/nwalign.rs:1967:17
[INFO] [stderr]      |
[INFO] [stderr] 1958 |                 i0 = false;
[INFO] [stderr]      |                 ---------- `i0` is overwritten here before the previous value is read
[INFO] [stderr] ...
[INFO] [stderr] 1967 |                 i0 = true;
[INFO] [stderr]      |                 ^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]     --> src/nwalign.rs:2566:13
[INFO] [stderr]      |
[INFO] [stderr] 2566 |         let mut rng = |st: &mut u64, m: usize| {
[INFO] [stderr]      |             ----^^^
[INFO] [stderr]      |             |
[INFO] [stderr]      |             help: remove this `mut`
[INFO] [stderr]      |
[INFO] [stderr]      = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: `dada2-rs` (bin "dada2-rs" test) generated 4 warnings (run `cargo fix --bin "dada2-rs" -p dada2-rs --tests` to apply 1 suggestion)
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 1m 24s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/release/deps/dada2_rs-ba109fb240da413f)
[INFO] [stdout] 
[INFO] [stdout] running 56 tests
[INFO] [stdout] test error_models::tests::test_accumulate_trans_sums_correctly ... ok
[INFO] [stdout] test chimera::tests::pooled_diagnostics_flags_plain_bimera ... ok
[INFO] [stdout] test chimera::tests::pooled_diagnostics_rejects_snp_variant ... ok
[INFO] [stdout] test derep::tests::checked_qual_sum_passes_through_in_range ... ok
[INFO] [stdout] test chimera::tests::pooled_diagnostics_detects_trimera ... ok
[INFO] [stdout] test error_models::tests::loess_config_default_and_r_dada2_presets ... ok
[INFO] [stdout] test error_models::tests::test_get_bad_bases_empty_input ... ok
[INFO] [stdout] test error_models::tests::test_inflate_err_increases_off_diagonal ... ok
[INFO] [stdout] test kmers::bench::bench_kmer_dist8 ... ignored
[INFO] [stdout] test error_models::tests::test_loess_errfun_shape ... ok
[INFO] [stdout] test error_models::tests::test_noqual_errfun_rows_sum_to_one ... ok
[INFO] [stdout] test derep::tests::checked_qual_sum_panics_on_overflow - should panic ... ok
[INFO] [stdout] test kmers::sparse_tests::sparse_dist_matches_dense ... ok
[INFO] [stdout] test error_models::tests::test_expand_err_matrix_diagonal ... ok
[INFO] [stdout] test nwalign::bench_align::bench_align_vectorized ... ignored
[INFO] [stdout] test kmers::sparse_tests::sparse_dist_overflow_matches_dense ... ok
[INFO] [stdout] test learn_errors::tests::learned_err_params_roundtrips_wfa_max_edits ... ok
[INFO] [stdout] test kmers::sparse_tests::sparse_reconstructs_dense ... ok
[INFO] [stdout] test learn_errors::tests::learned_err_params_defaults_wfa_max_edits_when_absent ... ok
[INFO] [stdout] test error_models::tests::test_external_errfun_propagates_nonzero_exit ... ok
[INFO] [stdout] test nwalign::tests::sweep_vectorized_parity ... ignored
[INFO] [stdout] test nwalign::tests::test_align_endsfree_one_sub ... ok
[INFO] [stdout] test nwalign::tests::test_align_endsfree_identical_short ... ok
[INFO] [stdout] test nwalign::tests::test_align_endsfree_one_gap ... ok
[INFO] [stdout] test nwalign::tests::test_vectorized_vs_endsfree_one_gap ... ok
[INFO] [stdout] test nwalign::tests::test_vectorized_vs_endsfree_one_sub ... ok
[INFO] [stdout] test nwalign::tests::wfa_cost_cap_converts_edits_to_cost ... ok
[INFO] [stdout] test remove_primers::tests::find_first_exact ... ok
[INFO] [stdout] test remove_primers::tests::find_first_left_boundary_overhang ... ok
[INFO] [stdout] test remove_primers::tests::find_iupac_primer ... ok
[INFO] [stdout] test remove_primers::tests::find_last_exact ... ok
[INFO] [stdout] test remove_primers::tests::find_last_right_boundary_overhang ... ok
[INFO] [stdout] test nwalign::tests::homo_gap_penalty_routes_to_homopolymer_aligner ... ok
[INFO] [stdout] test remove_primers::tests::find_with_mismatch ... ok
[INFO] [stdout] test remove_primers::tests::indel_exact_match_same_as_hamming ... ok
[INFO] [stdout] test remove_primers::tests::indel_last_match ... ok
[INFO] [stdout] test nwalign::tests::test_vectorized_vs_endsfree_different_lengths ... ok
[INFO] [stdout] test nwalign::tests::test_vectorized_vs_endsfree_identical ... ok
[INFO] [stdout] test remove_primers::tests::indel_single_deletion_in_read ... ok
[INFO] [stdout] test remove_primers::tests::iupac_rc_acgt ... ok
[INFO] [stdout] test remove_primers::tests::indel_single_insertion_in_read ... ok
[INFO] [stdout] test nwalign::tests::test_vectorized_vs_endsfree_divergent_240 ... ok
[INFO] [stdout] test remove_primers::tests::iupac_rc_lowercase ... ok
[INFO] [stdout] test remove_primers::tests::process_read_basic_trim ... ok
[INFO] [stdout] test remove_primers::tests::process_read_indel_mode_trims ... ok
[INFO] [stdout] test remove_primers::tests::process_read_no_primer_discarded ... ok
[INFO] [stdout] test remove_primers::tests::process_read_orient_flip ... ok
[INFO] [stdout] test summary::tests::complexity_of_a_homopolymer_is_one ... ok
[INFO] [stdout] test nwalign::tests::test_vectorized_vs_endsfree_equal_length_240 ... ok
[INFO] [stdout] test summary::tests::cumulative_ee_is_running_sum_of_per_base_error ... ok
[INFO] [stdout] test tests::match_genera_rules ... ok
[INFO] [stdout] test remove_primers::tests::iupac_ambig ... ok
[INFO] [stdout] test remove_primers::tests::iupac_exact ... ok
[INFO] [stdout] test remove_primers::tests::iupac_rc_ambig ... ok
[INFO] [stdout] test error_models::tests::test_external_errfun_roundtrip ... ok
[INFO] [stdout] test error_models::tests::test_external_errfun_rejects_invalid_probability ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 53 passed; 0 failed; 3 ignored; 0 measured; 0 filtered out; finished in 0.05s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/dada_pseudo.rs (/opt/rustwide/target/release/deps/dada_pseudo-a10795be3e947751)
[INFO] [stdout] 
[INFO] [stdout] running 13 tests
[INFO] [stdout] test dada_input_output_guards ... ok
[INFO] [stdout] test dada_failed_uniques_matches_map_nulls ... ok
[INFO] [stdout] test dada_from_fastq_matches_dada_from_derep_json ... ok
[INFO] [stdout] test derep_orders_by_abundance_then_lexical ... ok
[INFO] [stdout] test dada_multi_input_matches_per_file_runs ... ok
[INFO] [stdout] test dada_pooled_is_deterministic_across_threads ... ok
[INFO] [stdout] test dada_pseudo_is_deterministic_across_sample_jobs ... ok
[INFO] [stdout] test dada_pseudo_streaming_matches_cached ... ok
[INFO] [stdout] test dada_homo_gap_defaults_to_gap_penalty ... ok
[INFO] [stdout] test merge_pairs_rescue_unmerged_concatenates ... ok
[INFO] [stdout] test dada_pseudo_matches_manual_recipe ... ok
[INFO] [stdout] test merge_pairs_is_deterministic_across_threads ... ok
[INFO] [stdout] test dada_pseudo_output_feeds_downstream_steps ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 13 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 12.59s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1", kill_on_drop: false }`
[INFO] [stdout] 71677b49ec31d3ff069ff815af5f39c3ab30ab198923953a2942cc63306435e1
