[INFO] cloning repository https://github.com/bluenote-1577/sce-aligner
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/bluenote-1577/sce-aligner" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fsce-aligner", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fsce-aligner'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 626fc3bdaf20d8a570e63fdbd80e3eabe0baf698
[INFO] testing bluenote-1577/sce-aligner against beta-2025-09-21 for beta-1.91-2
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fsce-aligner" "/workspace/builds/worker-2-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/bluenote-1577/sce-aligner
[INFO] finished tweaking git repo https://github.com/bluenote-1577/sce-aligner
[INFO] tweaked toml for git repo https://github.com/bluenote-1577/sce-aligner written to /workspace/builds/worker-2-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/bluenote-1577/sce-aligner 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 git repo https://github.com/bluenote-1577/sce-aligner 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 }`
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[INFO] running `Command { std: "docker" "start" "-a" "034bbfbdc6c7518571d0f7c96a1ae37187ceec04efccdb5a4f03fdf555deccd1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "034bbfbdc6c7518571d0f7c96a1ae37187ceec04efccdb5a4f03fdf555deccd1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "034bbfbdc6c7518571d0f7c96a1ae37187ceec04efccdb5a4f03fdf555deccd1", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "start" "-a" "0d3956bea44cda0908fbbb768ac66b7653452976363f1f398e9136466150fd5c", kill_on_drop: false }`
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[INFO] [stderr]    Compiling intervallum v1.4.0
[INFO] [stderr]    Compiling rust-lapper v1.1.0
[INFO] [stderr]    Compiling nohash-hasher v0.2.0
[INFO] [stderr]    Compiling bio-types v0.13.0
[INFO] [stderr]    Compiling libwfa v0.1.2
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[INFO] [stderr]    Compiling nalgebra v0.29.0
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[INFO] [stderr]    Compiling multimap v0.8.3
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[INFO] [stderr]    Compiling statrs v0.16.0
[INFO] [stderr]    Compiling bio v1.1.0
[INFO] [stderr]    Compiling sce_aligner v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `fxhash::FxHashMap`
[INFO] [stdout]  --> src/file_io.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use fxhash::FxHashMap;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs::File`
[INFO] [stdout]  --> src/file_io.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use std::fs::File;
[INFO] [stdout]   |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `BufReader`, `BufWriter`, `Write`, and `self`
[INFO] [stdout]   --> src/file_io.rs:10:15
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::io::{self, BufReader, BufWriter, Write};
[INFO] [stdout]    |               ^^^^  ^^^^^^^^^  ^^^^^^^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::time::Instant`
[INFO] [stdout]  --> src/seeding.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::time::Instant;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Interval` and `Lapper`
[INFO] [stdout]  --> src/seeding.rs:6:19
[INFO] [stdout]   |
[INFO] [stdout] 6 | use rust_lapper::{Interval, Lapper};
[INFO] [stdout]   |                   ^^^^^^^^  ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `smallvec::SmallVec`
[INFO] [stdout]  --> src/seeding.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use smallvec::SmallVec;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `SubCommand`
[INFO] [stdout]  --> src/main.rs:2:22
[INFO] [stdout]   |
[INFO] [stdout] 2 | use clap::{App, Arg, SubCommand};
[INFO] [stdout]   |                      ^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `fxhash::FxHashSet`
[INFO] [stdout]  --> src/main.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use fxhash::FxHashSet;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Write` and `self`
[INFO] [stdout]   --> src/main.rs:12:15
[INFO] [stdout]    |
[INFO] [stdout] 12 | use std::io::{self, BufReader, BufWriter, Write};
[INFO] [stdout]    |               ^^^^                        ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::mem`
[INFO] [stdout]   --> src/main.rs:13:5
[INFO] [stdout]    |
[INFO] [stdout] 13 | use std::mem;
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around closure body
[INFO] [stdout]   --> src/main.rs:81:22
[INFO] [stdout]    |
[INFO] [stdout] 81 |             .map(|x| (*x as usize))
[INFO] [stdout]    |                      ^           ^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]    |
[INFO] [stdout] 81 -             .map(|x| (*x as usize))
[INFO] [stdout] 81 +             .map(|x| *x as usize)
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `print_all_debug`
[INFO] [stdout]   --> src/main.rs:57:9
[INFO] [stdout]    |
[INFO] [stdout] 57 |     let print_all_debug = false;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_print_all_debug`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `use_minimizers`
[INFO] [stdout]   --> src/main.rs:58:9
[INFO] [stdout]    |
[INFO] [stdout] 58 |     let use_minimizers = matches.is_present("minimizer");
[INFO] [stdout]    |         ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_use_minimizers`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `use_wfa`
[INFO] [stdout]   --> src/main.rs:59:9
[INFO] [stdout]    |
[INFO] [stdout] 59 |     let use_wfa = matches.is_present("wfa");
[INFO] [stdout]    |         ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_use_wfa`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `sketch`
[INFO] [stdout]   --> src/main.rs:60:9
[INFO] [stdout]    |
[INFO] [stdout] 60 |     let sketch = matches.is_present("sketch");
[INFO] [stdout]    |         ^^^^^^ help: if this is intentional, prefix it with an underscore: `_sketch`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `window`
[INFO] [stdout]   --> src/main.rs:98:9
[INFO] [stdout]    |
[INFO] [stdout] 98 |     let window = 2 * c - 1;
[INFO] [stdout]    |         ^^^^^^ help: if this is intentional, prefix it with an underscore: `_window`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `t`
[INFO] [stdout]   --> src/main.rs:99:9
[INFO] [stdout]    |
[INFO] [stdout] 99 |     let t = (k - s + 1) / 2 + 1;
[INFO] [stdout]    |         ^ help: if this is intentional, prefix it with an underscore: `_t`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `range`
[INFO] [stdout]    --> src/main.rs:342:17
[INFO] [stdout]     |
[INFO] [stdout] 342 |             let range = best_chain[0].ref_pos - best_chain[best_chain.len() - 1].ref_pos;
[INFO] [stdout]     |                 ^^^^^ help: if this is intentional, prefix it with an underscore: `_range`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `alignment`
[INFO] [stdout]    --> src/main.rs:430:21
[INFO] [stdout]     |
[INFO] [stdout] 430 |                 let alignment = aligner.global(&ref_slice, query_slice);
[INFO] [stdout]     |                     ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_alignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [optimized + debuginfo] target(s) in 2m 22s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: buf_redux v0.8.4, nom v5.1.2, partitions v0.2.4
[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" "0d3956bea44cda0908fbbb768ac66b7653452976363f1f398e9136466150fd5c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "0d3956bea44cda0908fbbb768ac66b7653452976363f1f398e9136466150fd5c", kill_on_drop: false }`
[INFO] [stdout] 0d3956bea44cda0908fbbb768ac66b7653452976363f1f398e9136466150fd5c
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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] 58632cf0f6cd77fea5e01fee6f7f2b4d82ac64b74b2882f52ab27caef33d9cf9
[INFO] running `Command { std: "docker" "start" "-a" "58632cf0f6cd77fea5e01fee6f7f2b4d82ac64b74b2882f52ab27caef33d9cf9", kill_on_drop: false }`
[INFO] [stderr]    Compiling sce_aligner v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `fxhash::FxHashMap`
[INFO] [stdout]  --> src/file_io.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use fxhash::FxHashMap;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs::File`
[INFO] [stdout]  --> src/file_io.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use std::fs::File;
[INFO] [stdout]   |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `BufReader`, `BufWriter`, `Write`, and `self`
[INFO] [stdout]   --> src/file_io.rs:10:15
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::io::{self, BufReader, BufWriter, Write};
[INFO] [stdout]    |               ^^^^  ^^^^^^^^^  ^^^^^^^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::time::Instant`
[INFO] [stdout]  --> src/seeding.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::time::Instant;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Interval` and `Lapper`
[INFO] [stdout]  --> src/seeding.rs:6:19
[INFO] [stdout]   |
[INFO] [stdout] 6 | use rust_lapper::{Interval, Lapper};
[INFO] [stdout]   |                   ^^^^^^^^  ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `smallvec::SmallVec`
[INFO] [stdout]  --> src/seeding.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use smallvec::SmallVec;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `SubCommand`
[INFO] [stdout]  --> src/main.rs:2:22
[INFO] [stdout]   |
[INFO] [stdout] 2 | use clap::{App, Arg, SubCommand};
[INFO] [stdout]   |                      ^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `fxhash::FxHashSet`
[INFO] [stdout]  --> src/main.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use fxhash::FxHashSet;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Write` and `self`
[INFO] [stdout]   --> src/main.rs:12:15
[INFO] [stdout]    |
[INFO] [stdout] 12 | use std::io::{self, BufReader, BufWriter, Write};
[INFO] [stdout]    |               ^^^^                        ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::mem`
[INFO] [stdout]   --> src/main.rs:13:5
[INFO] [stdout]    |
[INFO] [stdout] 13 | use std::mem;
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around closure body
[INFO] [stdout]   --> src/main.rs:81:22
[INFO] [stdout]    |
[INFO] [stdout] 81 |             .map(|x| (*x as usize))
[INFO] [stdout]    |                      ^           ^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]    |
[INFO] [stdout] 81 -             .map(|x| (*x as usize))
[INFO] [stdout] 81 +             .map(|x| *x as usize)
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `fxhash::FxHashMap`
[INFO] [stdout]  --> src/file_io.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use fxhash::FxHashMap;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs::File`
[INFO] [stdout]  --> src/file_io.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use std::fs::File;
[INFO] [stdout]   |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `BufReader`, `BufWriter`, `Write`, and `self`
[INFO] [stdout]   --> src/file_io.rs:10:15
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::io::{self, BufReader, BufWriter, Write};
[INFO] [stdout]    |               ^^^^  ^^^^^^^^^  ^^^^^^^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::time::Instant`
[INFO] [stdout]  --> src/seeding.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::time::Instant;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Interval` and `Lapper`
[INFO] [stdout]  --> src/seeding.rs:6:19
[INFO] [stdout]   |
[INFO] [stdout] 6 | use rust_lapper::{Interval, Lapper};
[INFO] [stdout]   |                   ^^^^^^^^  ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `smallvec::SmallVec`
[INFO] [stdout]  --> src/seeding.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use smallvec::SmallVec;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `print_all_debug`
[INFO] [stdout]   --> src/main.rs:57:9
[INFO] [stdout]    |
[INFO] [stdout] 57 |     let print_all_debug = false;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_print_all_debug`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `use_minimizers`
[INFO] [stdout]   --> src/main.rs:58:9
[INFO] [stdout]    |
[INFO] [stdout] 58 |     let use_minimizers = matches.is_present("minimizer");
[INFO] [stdout]    |         ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_use_minimizers`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `use_wfa`
[INFO] [stdout]   --> src/main.rs:59:9
[INFO] [stdout]    |
[INFO] [stdout] 59 |     let use_wfa = matches.is_present("wfa");
[INFO] [stdout]    |         ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_use_wfa`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `sketch`
[INFO] [stdout]   --> src/main.rs:60:9
[INFO] [stdout]    |
[INFO] [stdout] 60 |     let sketch = matches.is_present("sketch");
[INFO] [stdout]    |         ^^^^^^ help: if this is intentional, prefix it with an underscore: `_sketch`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `window`
[INFO] [stdout]   --> src/main.rs:98:9
[INFO] [stdout]    |
[INFO] [stdout] 98 |     let window = 2 * c - 1;
[INFO] [stdout]    |         ^^^^^^ help: if this is intentional, prefix it with an underscore: `_window`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `t`
[INFO] [stdout]   --> src/main.rs:99:9
[INFO] [stdout]    |
[INFO] [stdout] 99 |     let t = (k - s + 1) / 2 + 1;
[INFO] [stdout]    |         ^ help: if this is intentional, prefix it with an underscore: `_t`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `range`
[INFO] [stdout]    --> src/main.rs:342:17
[INFO] [stdout]     |
[INFO] [stdout] 342 |             let range = best_chain[0].ref_pos - best_chain[best_chain.len() - 1].ref_pos;
[INFO] [stdout]     |                 ^^^^^ help: if this is intentional, prefix it with an underscore: `_range`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `alignment`
[INFO] [stdout]    --> src/main.rs:430:21
[INFO] [stdout]     |
[INFO] [stdout] 430 |                 let alignment = aligner.global(&ref_slice, query_slice);
[INFO] [stdout]     |                     ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_alignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [optimized + debuginfo] target(s) in 2.47s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: buf_redux v0.8.4, nom v5.1.2, partitions v0.2.4
[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" "58632cf0f6cd77fea5e01fee6f7f2b4d82ac64b74b2882f52ab27caef33d9cf9", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "58632cf0f6cd77fea5e01fee6f7f2b4d82ac64b74b2882f52ab27caef33d9cf9", kill_on_drop: false }`
[INFO] [stdout] 58632cf0f6cd77fea5e01fee6f7f2b4d82ac64b74b2882f52ab27caef33d9cf9
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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] 14e2f3e8fac81cfb5cc5b23175692aeac55c3ab9e4682271b0230e49dbd4e20e
[INFO] running `Command { std: "docker" "start" "-a" "14e2f3e8fac81cfb5cc5b23175692aeac55c3ab9e4682271b0230e49dbd4e20e", kill_on_drop: false }`
[INFO] [stderr] warning: unused import: `fxhash::FxHashMap`
[INFO] [stderr]  --> src/file_io.rs:3:5
[INFO] [stderr]   |
[INFO] [stderr] 3 | use fxhash::FxHashMap;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::fs::File`
[INFO] [stderr]  --> src/file_io.rs:9:5
[INFO] [stderr]   |
[INFO] [stderr] 9 | use std::fs::File;
[INFO] [stderr]   |     ^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused imports: `BufReader`, `BufWriter`, `Write`, and `self`
[INFO] [stderr]   --> src/file_io.rs:10:15
[INFO] [stderr]    |
[INFO] [stderr] 10 | use std::io::{self, BufReader, BufWriter, Write};
[INFO] [stderr]    |               ^^^^  ^^^^^^^^^  ^^^^^^^^^  ^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::time::Instant`
[INFO] [stderr]  --> src/seeding.rs:2:5
[INFO] [stderr]   |
[INFO] [stderr] 2 | use std::time::Instant;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused imports: `Interval` and `Lapper`
[INFO] [stderr]  --> src/seeding.rs:6:19
[INFO] [stderr]   |
[INFO] [stderr] 6 | use rust_lapper::{Interval, Lapper};
[INFO] [stderr]   |                   ^^^^^^^^  ^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `smallvec::SmallVec`
[INFO] [stderr]  --> src/seeding.rs:7:5
[INFO] [stderr]   |
[INFO] [stderr] 7 | use smallvec::SmallVec;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: `sce_aligner` (lib) generated 6 warnings (run `cargo fix --lib -p sce_aligner` to apply 6 suggestions)
[INFO] [stderr] warning: `sce_aligner` (lib test) generated 6 warnings (6 duplicates)
[INFO] [stderr] warning: unused import: `SubCommand`
[INFO] [stderr]  --> src/main.rs:2:22
[INFO] [stderr]   |
[INFO] [stderr] 2 | use clap::{App, Arg, SubCommand};
[INFO] [stderr]   |                      ^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `fxhash::FxHashSet`
[INFO] [stderr]  --> src/main.rs:3:5
[INFO] [stderr]   |
[INFO] [stderr] 3 | use fxhash::FxHashSet;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused imports: `Write` and `self`
[INFO] [stderr]   --> src/main.rs:12:15
[INFO] [stderr]    |
[INFO] [stderr] 12 | use std::io::{self, BufReader, BufWriter, Write};
[INFO] [stderr]    |               ^^^^                        ^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::mem`
[INFO] [stderr]   --> src/main.rs:13:5
[INFO] [stderr]    |
[INFO] [stderr] 13 | use std::mem;
[INFO] [stderr]    |     ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unnecessary parentheses around closure body
[INFO] [stderr]   --> src/main.rs:81:22
[INFO] [stderr]    |
[INFO] [stderr] 81 |             .map(|x| (*x as usize))
[INFO] [stderr]    |                      ^           ^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] help: remove these parentheses
[INFO] [stderr]    |
[INFO] [stderr] 81 -             .map(|x| (*x as usize))
[INFO] [stderr] 81 +             .map(|x| *x as usize)
[INFO] [stderr]    |
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `print_all_debug`
[INFO] [stderr]   --> src/main.rs:57:9
[INFO] [stderr]    |
[INFO] [stderr] 57 |     let print_all_debug = false;
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_print_all_debug`
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `use_minimizers`
[INFO] [stderr]   --> src/main.rs:58:9
[INFO] [stderr]    |
[INFO] [stderr] 58 |     let use_minimizers = matches.is_present("minimizer");
[INFO] [stderr]    |         ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_use_minimizers`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `use_wfa`
[INFO] [stderr]   --> src/main.rs:59:9
[INFO] [stderr]    |
[INFO] [stderr] 59 |     let use_wfa = matches.is_present("wfa");
[INFO] [stderr]    |         ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_use_wfa`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `sketch`
[INFO] [stderr]   --> src/main.rs:60:9
[INFO] [stderr]    |
[INFO] [stderr] 60 |     let sketch = matches.is_present("sketch");
[INFO] [stderr]    |         ^^^^^^ help: if this is intentional, prefix it with an underscore: `_sketch`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `window`
[INFO] [stderr]   --> src/main.rs:98:9
[INFO] [stderr]    |
[INFO] [stderr] 98 |     let window = 2 * c - 1;
[INFO] [stderr]    |         ^^^^^^ help: if this is intentional, prefix it with an underscore: `_window`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `t`
[INFO] [stderr]   --> src/main.rs:99:9
[INFO] [stderr]    |
[INFO] [stderr] 99 |     let t = (k - s + 1) / 2 + 1;
[INFO] [stderr]    |         ^ help: if this is intentional, prefix it with an underscore: `_t`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `range`
[INFO] [stderr]    --> src/main.rs:342:17
[INFO] [stderr]     |
[INFO] [stderr] 342 |             let range = best_chain[0].ref_pos - best_chain[best_chain.len() - 1].ref_pos;
[INFO] [stderr]     |                 ^^^^^ help: if this is intentional, prefix it with an underscore: `_range`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `alignment`
[INFO] [stderr]    --> src/main.rs:430:21
[INFO] [stderr]     |
[INFO] [stderr] 430 |                 let alignment = aligner.global(&ref_slice, query_slice);
[INFO] [stderr]     |                     ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_alignment`
[INFO] [stderr] 
[INFO] [stderr] warning: `sce_aligner` (bin "sce_aligner" test) generated 13 warnings (run `cargo fix --bin "sce_aligner" --tests` to apply 5 suggestions)
[INFO] [stderr]     Finished `test` profile [optimized + debuginfo] target(s) in 0.20s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: buf_redux v0.8.4, nom v5.1.2, partitions v0.2.4
[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/lib.rs (/opt/rustwide/target/debug/deps/sce_aligner-9769c3e20efbe76d)
[INFO] [stdout] 
[INFO] [stdout] running 7 tests
[INFO] [stdout] test avl_tree::tests::empty_tree ... ok
[INFO] [stdout] test avl_tree::tests::insert_node ... ok
[INFO] [stdout] test avl_tree::tests::insert_right_rot ... ok
[INFO] [stdout] test avl_tree::tests::right_left_rot ... ok
[INFO] [stdout] test avl_tree::tests::insert_left_rot ... ok
[INFO] [stdout] test avl_tree::tests::left_right_rot ... ok
[INFO] [stdout] test avl_tree::tests::random_values ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.43s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/sce_aligner-9a8fa9501b0c0300)
[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]    Doc-tests sce_aligner
[INFO] [stdout] 
[INFO] [stdout] running 5 tests
[INFO] [stdout] test src/avl_tree.rs - avl_tree::SearchTree<T>::new (line 37) ... FAILED
[INFO] [stdout] test src/avl_tree.rs - avl_tree::SearchTree<T>::insert (line 84) ... FAILED
[INFO] [stdout] test src/avl_tree.rs - avl_tree::SearchTree<T>::iter (line 332) ... FAILED
[INFO] [stdout] test src/avl_tree.rs - avl_tree::SearchTree<T>::contains (line 66) ... FAILED
[INFO] [stdout] test src/avl_tree.rs - avl_tree::SearchTree<T>::is_empty (line 52) ... FAILED
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout] 
[INFO] [stdout] ---- src/avl_tree.rs - avl_tree::SearchTree<T>::new (line 37) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `avltree`
[INFO] [stdout]  --> src/avl_tree.rs:38:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use avltree::SearchTree;
[INFO] [stdout]   |     ^^^^^^^ use of unresolved module or unlinked crate `avltree`
[INFO] [stdout]   |
[INFO] [stdout]   = help: if you wanted to use a crate named `avltree`, use `cargo add avltree` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/avl_tree.rs - avl_tree::SearchTree<T>::insert (line 84) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `avltree`
[INFO] [stdout]  --> src/avl_tree.rs:85:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use avltree::SearchTree;
[INFO] [stdout]   |     ^^^^^^^ use of unresolved module or unlinked crate `avltree`
[INFO] [stdout]   |
[INFO] [stdout]   = help: if you wanted to use a crate named `avltree`, use `cargo add avltree` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/avl_tree.rs - avl_tree::SearchTree<T>::iter (line 332) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `avltree`
[INFO] [stdout]  --> src/avl_tree.rs:333:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use avltree::SearchTree;
[INFO] [stdout]   |     ^^^^^^^ use of unresolved module or unlinked crate `avltree`
[INFO] [stdout]   |
[INFO] [stdout]   = help: if you wanted to use a crate named `avltree`, use `cargo add avltree` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/avl_tree.rs - avl_tree::SearchTree<T>::contains (line 66) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `avltree`
[INFO] [stdout]  --> src/avl_tree.rs:67:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use avltree::SearchTree;
[INFO] [stdout]   |     ^^^^^^^ use of unresolved module or unlinked crate `avltree`
[INFO] [stdout]   |
[INFO] [stdout]   = help: if you wanted to use a crate named `avltree`, use `cargo add avltree` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/avl_tree.rs - avl_tree::SearchTree<T>::is_empty (line 52) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `avltree`
[INFO] [stdout]  --> src/avl_tree.rs:53:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use avltree::SearchTree;
[INFO] [stdout]   |     ^^^^^^^ use of unresolved module or unlinked crate `avltree`
[INFO] [stdout]   |
[INFO] [stdout]   = help: if you wanted to use a crate named `avltree`, use `cargo add avltree` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout]     src/avl_tree.rs - avl_tree::SearchTree<T>::contains (line 66)
[INFO] [stdout]     src/avl_tree.rs - avl_tree::SearchTree<T>::insert (line 84)
[INFO] [stdout]     src/avl_tree.rs - avl_tree::SearchTree<T>::is_empty (line 52)
[INFO] [stdout]     src/avl_tree.rs - avl_tree::SearchTree<T>::iter (line 332)
[INFO] [stdout]     src/avl_tree.rs - avl_tree::SearchTree<T>::new (line 37)
[INFO] [stdout] 
[INFO] [stdout] test result: FAILED. 0 passed; 5 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.18s
[INFO] [stdout] 
[INFO] [stderr] error: doctest failed, to rerun pass `--doc`
[INFO] running `Command { std: "docker" "inspect" "14e2f3e8fac81cfb5cc5b23175692aeac55c3ab9e4682271b0230e49dbd4e20e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "14e2f3e8fac81cfb5cc5b23175692aeac55c3ab9e4682271b0230e49dbd4e20e", kill_on_drop: false }`
[INFO] [stdout] 14e2f3e8fac81cfb5cc5b23175692aeac55c3ab9e4682271b0230e49dbd4e20e