[INFO] fetching crate rustynuc 0.3.0...
[INFO] testing rustynuc-0.3.0 against beta-2025-09-21 for beta-1.91-3
[INFO] extracting crate rustynuc 0.3.0 into /workspace/builds/worker-3-tc2/source
[INFO] started tweaking crates.io crate rustynuc 0.3.0
[INFO] finished tweaking crates.io crate rustynuc 0.3.0
[INFO] tweaked toml for crates.io crate rustynuc 0.3.0 written to /workspace/builds/worker-3-tc2/source/Cargo.toml
[INFO] validating manifest of crates.io crate rustynuc 0.3.0 on toolchain beta-2025-09-21
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2025-09-21" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate rustynuc 0.3.0 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" "+beta-2025-09-21" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/source:/opt/rustwide/workdir:ro,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" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 6ac2cb00945fa36af9f614dc20b7a4d7701d527409d3aaf22fc4e4afb0400afc
[INFO] running `Command { std: "docker" "start" "-a" "6ac2cb00945fa36af9f614dc20b7a4d7701d527409d3aaf22fc4e4afb0400afc", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "6ac2cb00945fa36af9f614dc20b7a4d7701d527409d3aaf22fc4e4afb0400afc", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "6ac2cb00945fa36af9f614dc20b7a4d7701d527409d3aaf22fc4e4afb0400afc", kill_on_drop: false }`
[INFO] [stdout] 6ac2cb00945fa36af9f614dc20b7a4d7701d527409d3aaf22fc4e4afb0400afc
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/source:/opt/rustwide/workdir:ro,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" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-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" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 397fbf1b0a2e670eca6eb7bbb2fb6c9bfd20d186a6543a6b442c6a4c585cf202
[INFO] running `Command { std: "docker" "start" "-a" "397fbf1b0a2e670eca6eb7bbb2fb6c9bfd20d186a6543a6b442c6a4c585cf202", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.24
[INFO] [stderr]    Compiling libc v0.2.80
[INFO] [stderr]    Compiling syn v1.0.53
[INFO] [stderr]    Compiling serde_derive v1.0.118
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling serde v1.0.118
[INFO] [stderr]    Compiling memchr v2.3.4
[INFO] [stderr]    Compiling crossbeam-utils v0.8.1
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling memoffset v0.6.1
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling const_fn v0.4.3
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling tinyvec_macros v0.1.0
[INFO] [stderr]    Compiling unicode-segmentation v1.7.1
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]    Compiling tinyvec v1.1.0
[INFO] [stderr]    Compiling thread_local v1.0.1
[INFO] [stderr]    Compiling miniz_oxide v0.4.3
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling num-complex v0.2.4
[INFO] [stderr]    Compiling regex-syntax v0.6.21
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling doc-comment v0.3.3
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]    Compiling crc32fast v1.2.1
[INFO] [stderr]    Compiling heck v0.3.1
[INFO] [stderr]    Compiling rayon-core v1.9.0
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[INFO] [stderr]    Compiling ndarray v0.13.1
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[INFO] [stderr]    Compiling percent-encoding v2.1.0
[INFO] [stderr]    Compiling rawpointer v0.2.1
[INFO] [stderr]    Compiling either v1.6.1
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[INFO] [stderr]    Compiling rand_core v0.5.1
[INFO] [stderr]    Compiling cc v1.0.66
[INFO] [stderr]    Compiling csv-core v0.1.10
[INFO] [stderr]    Compiling log v0.4.11
[INFO] [stderr]    Compiling crossbeam-channel v0.5.0
[INFO] [stderr]    Compiling rand_chacha v0.2.2
[INFO] [stderr]    Compiling rayon v1.5.0
[INFO] [stderr]    Compiling unicode-normalization v0.1.16
[INFO] [stderr]    Compiling fixedbitset v0.1.9
[INFO] [stderr]    Compiling ordermap v0.3.5
[INFO] [stderr]    Compiling num-traits v0.1.43
[INFO] [stderr]    Compiling bio v0.30.1
[INFO] [stderr]    Compiling rand v0.7.3
[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling bit-vec v0.6.3
[INFO] [stderr]    Compiling itoa v0.4.6
[INFO] [stderr]    Compiling flate2 v1.0.19
[INFO] [stderr]    Compiling petgraph v0.4.13
[INFO] [stderr]    Compiling enum_primitive v0.1.1
[INFO] [stderr]    Compiling bit-set v0.5.2
[INFO] [stderr]    Compiling ordered-float v1.1.0
[INFO] [stderr]    Compiling itertools-num v0.1.3
[INFO] [stderr]    Compiling approx v0.3.2
[INFO] [stderr]    Compiling itertools v0.9.0
[INFO] [stderr]    Compiling fxhash v0.2.1
[INFO] [stderr]    Compiling ieee754 v0.2.6
[INFO] [stderr]    Compiling strum v0.18.0
[INFO] [stderr]    Compiling linear-map v1.2.0
[INFO] [stderr]    Compiling bytecount v0.6.2
[INFO] [stderr]    Compiling env_logger v0.7.1
[INFO] [stderr]    Compiling fishers_exact v1.0.1
[INFO] [stderr]    Compiling idna v0.2.0
[INFO] [stderr]    Compiling url v2.2.0
[INFO] [stderr]    Compiling libz-sys v1.1.2
[INFO] [stderr]    Compiling hts-sys v1.10.3
[INFO] [stderr]    Compiling statrs v0.12.0
[INFO] [stderr]    Compiling regex v1.4.2
[INFO] [stderr]    Compiling thiserror-impl v1.0.22
[INFO] [stderr]    Compiling derive-new v0.5.8
[INFO] [stderr]    Compiling snafu-derive v0.6.10
[INFO] [stderr]    Compiling strum_macros v0.18.0
[INFO] [stderr]    Compiling structopt-derive v0.4.14
[INFO] [stderr]    Compiling getset v0.0.9
[INFO] [stderr]    Compiling snafu v0.6.10
[INFO] [stderr]    Compiling thiserror v1.0.22
[INFO] [stderr]    Compiling niffler v2.2.0
[INFO] [stderr]    Compiling vec_map v0.8.2
[INFO] [stderr]    Compiling bio-types v0.7.0
[INFO] [stderr]    Compiling bstr v0.2.14
[INFO] [stderr]    Compiling multimap v0.6.0
[INFO] [stderr]    Compiling clap v2.33.3
[INFO] [stderr]    Compiling csv v1.1.5
[INFO] [stderr]    Compiling rust-htslib v0.31.0
[INFO] [stderr]    Compiling structopt v0.3.21
[INFO] [stderr]    Compiling rustynuc v0.3.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: struct `NucleotideCount` is never constructed
[INFO] [stdout]   --> src/alignment.rs:66:12
[INFO] [stdout]    |
[INFO] [stdout] 66 | pub struct NucleotideCount(pub HashMap<u8, u32>);
[INFO] [stdout]    |            ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout] note: the lint level is defined here
[INFO] [stdout]   --> src/alignment.rs:2:20
[INFO] [stdout]    |
[INFO] [stdout]  2 | #![deny(dead_code, unused)]
[INFO] [stdout]    |                    ^^^^^^
[INFO] [stdout]    = note: `#[warn(dead_code)]` implied by `#[warn(unused)]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 42.78s
[INFO] running `Command { std: "docker" "inspect" "397fbf1b0a2e670eca6eb7bbb2fb6c9bfd20d186a6543a6b442c6a4c585cf202", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "397fbf1b0a2e670eca6eb7bbb2fb6c9bfd20d186a6543a6b442c6a4c585cf202", kill_on_drop: false }`
[INFO] [stdout] 397fbf1b0a2e670eca6eb7bbb2fb6c9bfd20d186a6543a6b442c6a4c585cf202
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/source:/opt/rustwide/workdir:ro,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" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-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" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] c2832fbdd6b937075da934bbf26c05a558a3d872cb7e956c9d42908b02b8ecca
[INFO] running `Command { std: "docker" "start" "-a" "c2832fbdd6b937075da934bbf26c05a558a3d872cb7e956c9d42908b02b8ecca", kill_on_drop: false }`
[INFO] [stderr]    Compiling semver-parser v0.7.0
[INFO] [stderr]    Compiling serde_json v1.0.60
[INFO] [stderr]    Compiling predicates-core v1.0.0
[INFO] [stderr]    Compiling float-cmp v0.8.0
[INFO] [stderr]    Compiling half v1.6.0
[INFO] [stderr]    Compiling normalize-line-endings v0.3.0
[INFO] [stderr]    Compiling treeline v0.1.0
[INFO] [stderr]    Compiling difference v2.0.0
[INFO] [stderr]    Compiling walkdir v2.3.1
[INFO] [stderr]    Compiling plotters v0.2.15
[INFO] [stderr]    Compiling wait-timeout v0.2.0
[INFO] [stderr]    Compiling oorandom v11.1.3
[INFO] [stdout] warning: struct `NucleotideCount` is never constructed
[INFO] [stdout]   --> src/alignment.rs:66:12
[INFO] [stdout]    |
[INFO] [stdout] 66 | pub struct NucleotideCount(pub HashMap<u8, u32>);
[INFO] [stdout]    |            ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout] note: the lint level is defined here
[INFO] [stdout]   --> src/alignment.rs:2:20
[INFO] [stdout]    |
[INFO] [stdout]  2 | #![deny(dead_code, unused)]
[INFO] [stdout]    |                    ^^^^^^
[INFO] [stdout]    = note: `#[warn(dead_code)]` implied by `#[warn(unused)]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]    Compiling serde_cbor v0.11.1
[INFO] [stderr]    Compiling predicates-tree v1.0.0
[INFO] [stderr]    Compiling predicates v1.0.5
[INFO] [stderr]    Compiling semver v0.9.0
[INFO] [stderr]    Compiling rustc_version v0.2.3
[INFO] [stderr]    Compiling cast v0.2.3
[INFO] [stderr]    Compiling assert_cmd v1.0.2
[INFO] [stderr]    Compiling criterion-plot v0.4.3
[INFO] [stderr]    Compiling tinytemplate v1.1.0
[INFO] [stderr]    Compiling criterion v0.3.3
[INFO] [stderr]    Compiling rustynuc v0.3.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: struct `NucleotideCount` is never constructed
[INFO] [stdout]   --> src/alignment.rs:66:12
[INFO] [stdout]    |
[INFO] [stdout] 66 | pub struct NucleotideCount(pub HashMap<u8, u32>);
[INFO] [stdout]    |            ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout] note: the lint level is defined here
[INFO] [stdout]   --> src/alignment.rs:2:20
[INFO] [stdout]    |
[INFO] [stdout]  2 | #![deny(dead_code, unused)]
[INFO] [stdout]    |                    ^^^^^^
[INFO] [stdout]    = note: `#[warn(dead_code)]` implied by `#[warn(unused)]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 10.79s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: criterion v0.3.3
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] running `Command { std: "docker" "inspect" "c2832fbdd6b937075da934bbf26c05a558a3d872cb7e956c9d42908b02b8ecca", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c2832fbdd6b937075da934bbf26c05a558a3d872cb7e956c9d42908b02b8ecca", kill_on_drop: false }`
[INFO] [stdout] c2832fbdd6b937075da934bbf26c05a558a3d872cb7e956c9d42908b02b8ecca
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/source:/opt/rustwide/workdir:ro,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" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-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" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] e76da61becf7f926be695cdef72c94e015d0aa5d93709c8c3e36f44c0f5dd71d
[INFO] running `Command { std: "docker" "start" "-a" "e76da61becf7f926be695cdef72c94e015d0aa5d93709c8c3e36f44c0f5dd71d", kill_on_drop: false }`
[INFO] [stderr] warning: struct `NucleotideCount` is never constructed
[INFO] [stderr]   --> src/alignment.rs:66:12
[INFO] [stderr]    |
[INFO] [stderr] 66 | pub struct NucleotideCount(pub HashMap<u8, u32>);
[INFO] [stderr]    |            ^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] note: the lint level is defined here
[INFO] [stderr]   --> src/alignment.rs:2:20
[INFO] [stderr]    |
[INFO] [stderr]  2 | #![deny(dead_code, unused)]
[INFO] [stderr]    |                    ^^^^^^
[INFO] [stderr]    = note: `#[warn(dead_code)]` implied by `#[warn(unused)]`
[INFO] [stderr] 
[INFO] [stderr] warning: `rustynuc` (bin "rustynuc") generated 1 warning
[INFO] [stderr] warning: `rustynuc` (bin "rustynuc" test) generated 1 warning (1 duplicate)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.22s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: criterion v0.3.3
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/rustynuc-3d0078bafb82469c)
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/tests.rs (/opt/rustwide/target/debug/deps/tests-77f6928d4df5587e)
[INFO] [stdout] 
[INFO] [stdout] running 14 tests
[INFO] [stdout] test cli_no_args ... ok
[INFO] [stdout] test cli_no_such_file ... ok
[INFO] [stdout] test cli_dont_warn_as_no_mnp ... ok
[INFO] [stdout] test cli_warn_about_mnp ... ok
[INFO] [stdout] test cli_oxog_bcf ... ok
[INFO] [stdout] test cli_oxog_bcf_skip_fishers ... ok
[INFO] [stdout] test cli_normal_bam ... ok
[INFO] [stdout] test cli_oxog_bam ... ok
[INFO] [stdout] test cli_not_false_positive_oxog_one_freq_above_af_either_pass ... ok
[INFO] [stdout] test cli_not_false_positive_as_they_pass_either_above_af ... ok
[INFO] [stdout] test cli_not_oxog_as_above_either_pass ... ok
[INFO] [stdout] test cli_print_all ... ok
[INFO] [stdout] test cli_false_positive_oxog_as_not_above_either_or_both ... ok
[INFO] [stdout] test cli_af_not_above_one ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 14 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 1.04s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "e76da61becf7f926be695cdef72c94e015d0aa5d93709c8c3e36f44c0f5dd71d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e76da61becf7f926be695cdef72c94e015d0aa5d93709c8c3e36f44c0f5dd71d", kill_on_drop: false }`
[INFO] [stdout] e76da61becf7f926be695cdef72c94e015d0aa5d93709c8c3e36f44c0f5dd71d