[INFO] cloning repository https://github.com/ARU-life-sciences/rep
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/ARU-life-sciences/rep" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FARU-life-sciences%2Frep", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FARU-life-sciences%2Frep'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] c09f881d4ece9ee64eb28a0ea02de2d7ca48c923
[INFO] checking ARU-life-sciences/rep against try#a3dffdb3a32d0dedc198f9de7d43173f3eb6727b for pr-136303
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FARU-life-sciences%2Frep" "/workspace/builds/worker-0-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/ARU-life-sciences/rep on toolchain a3dffdb3a32d0dedc198f9de7d43173f3eb6727b
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+a3dffdb3a32d0dedc198f9de7d43173f3eb6727b" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/ARU-life-sciences/rep
[INFO] finished tweaking git repo https://github.com/ARU-life-sciences/rep
[INFO] tweaked toml for git repo https://github.com/ARU-life-sciences/rep written to /workspace/builds/worker-0-tc2/source/Cargo.toml
[INFO] crate git repo https://github.com/ARU-life-sciences/rep 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" "+a3dffdb3a32d0dedc198f9de7d43173f3eb6727b" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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:c80049f3b88b82089a44e0f06d0d6029d44b96b7257e55a1cd63dbc9f4c33334" "/opt/rustwide/cargo-home/bin/cargo" "+a3dffdb3a32d0dedc198f9de7d43173f3eb6727b" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 3346801ad3aa12f8549f4a8dbd28701749a835cd0a128a7640a0c7c6908fb9bf
[INFO] running `Command { std: "docker" "start" "-a" "3346801ad3aa12f8549f4a8dbd28701749a835cd0a128a7640a0c7c6908fb9bf", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "3346801ad3aa12f8549f4a8dbd28701749a835cd0a128a7640a0c7c6908fb9bf", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "3346801ad3aa12f8549f4a8dbd28701749a835cd0a128a7640a0c7c6908fb9bf", kill_on_drop: false }`
[INFO] [stdout] 3346801ad3aa12f8549f4a8dbd28701749a835cd0a128a7640a0c7c6908fb9bf
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-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:c80049f3b88b82089a44e0f06d0d6029d44b96b7257e55a1cd63dbc9f4c33334" "/opt/rustwide/cargo-home/bin/cargo" "+a3dffdb3a32d0dedc198f9de7d43173f3eb6727b" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 842027efb2548335023e33ec46904ada5113ebfbf7a1bd133f1473a9809803ac
[INFO] running `Command { std: "docker" "start" "-a" "842027efb2548335023e33ec46904ada5113ebfbf7a1bd133f1473a9809803ac", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.79
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling libc v0.2.153
[INFO] [stderr]     Checking memchr v2.7.1
[INFO] [stderr]    Compiling serde v1.0.197
[INFO] [stderr]     Checking bytemuck v1.15.0
[INFO] [stderr]    Compiling rustversion v1.0.14
[INFO] [stderr]    Compiling matrixmultiply v0.3.8
[INFO] [stderr]    Compiling num-rational v0.4.1
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling thiserror v1.0.58
[INFO] [stderr]     Checking utf8parse v0.2.1
[INFO] [stderr]     Checking regex-syntax v0.8.2
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking num-complex v0.4.5
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking anstyle-parse v0.2.3
[INFO] [stderr]     Checking anstyle v1.0.6
[INFO] [stderr]     Checking safe_arch v0.7.1
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking colorchoice v1.0.0
[INFO] [stderr]    Compiling anyhow v1.0.81
[INFO] [stderr]     Checking anstyle-query v1.0.2
[INFO] [stderr]     Checking hashbrown v0.14.3
[INFO] [stderr]     Checking either v1.10.0
[INFO] [stderr]     Checking byteorder v1.5.0
[INFO] [stderr]     Checking itoa v1.0.10
[INFO] [stderr]     Checking anstream v0.6.13
[INFO] [stderr]     Checking clap_lex v0.7.0
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking bit-vec v0.6.3
[INFO] [stderr]     Checking strsim v0.11.0
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]     Checking csv-core v0.1.11
[INFO] [stderr]     Checking itertools v0.11.0
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking wide v0.7.15
[INFO] [stderr]     Checking clap_builder v4.5.2
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v3.9.2
[INFO] [stderr]     Checking bytecount v0.6.7
[INFO] [stderr]     Checking bit-set v0.5.3
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking strum v0.25.0
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking walkdir v2.5.0
[INFO] [stderr]    Compiling quote v1.0.35
[INFO] [stderr]     Checking indexmap v2.2.5
[INFO] [stderr]     Checking getrandom v0.2.12
[INFO] [stderr]    Compiling syn v2.0.53
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking rand_chacha v0.3.1
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[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking regex-automata v0.4.6
[INFO] [stderr]     Checking simba v0.6.0
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking clap v4.5.2
[INFO] [stderr]     Checking regex v1.10.3
[INFO] [stderr]    Compiling serde_derive v1.0.197
[INFO] [stderr]    Compiling thiserror-impl v1.0.58
[INFO] [stderr]    Compiling strum_macros v0.25.3
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]     Checking bio-types v1.0.1
[INFO] [stderr]     Checking nalgebra v0.29.0
[INFO] [stderr]     Checking csv v1.3.0
[INFO] [stderr]     Checking multimap v0.9.1
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking vec_map v0.8.2
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[INFO] [stderr]     Checking bio v1.5.0
[INFO] [stderr]     Checking rep v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `borrow::Cow`
[INFO] [stdout]  --> src/rm_curation_pipeline.rs:2:11
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::{borrow::Cow, fs, io, path::PathBuf};
[INFO] [stdout]   |           ^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `borrow::Cow`
[INFO] [stdout]  --> src/rm_curation_pipeline.rs:2:11
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::{borrow::Cow, fs, io, path::PathBuf};
[INFO] [stdout]   |           ^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `flank`
[INFO] [stdout]   --> src/rm_curation_pipeline.rs:81:9
[INFO] [stdout]    |
[INFO] [stdout] 81 |     let flank = 2000;
[INFO] [stdout]    |         ^^^^^ help: if this is intentional, prefix it with an underscore: `_flank`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `digits`
[INFO] [stdout]   --> src/rm_curation_pipeline.rs:84:9
[INFO] [stdout]    |
[INFO] [stdout] 84 |     let digits = 5;
[INFO] [stdout]    |         ^^^^^^ help: if this is intentional, prefix it with an underscore: `_digits`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `temp_mafft`
[INFO] [stdout]   --> src/rm_curation_pipeline.rs:99:9
[INFO] [stdout]    |
[INFO] [stdout] 99 |     let temp_mafft = matches.configure.join(INTERMEDIATE).join("tempMafft.txt");
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_temp_mafft`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `rmdl_library_reader`
[INFO] [stdout]    --> src/rm_curation_pipeline.rs:207:9
[INFO] [stdout]     |
[INFO] [stdout] 207 |     let rmdl_library_reader = fasta::Reader::from_file(rmdl_library)?;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_rmdl_library_reader`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `unique_hits`
[INFO] [stdout]    --> src/rm_curation_pipeline.rs:236:13
[INFO] [stdout]     |
[INFO] [stdout] 236 |         let unique_hits = top_blast_hits.filter_unique_combinations();
[INFO] [stdout]     |             ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_unique_hits`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `maxhitdist`
[INFO] [stdout]    --> src/rm_curation_pipeline.rs:172:5
[INFO] [stdout]     |
[INFO] [stdout] 172 |     maxhitdist: i32,
[INFO] [stdout]     |     ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_maxhitdist`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `minfrac`
[INFO] [stdout]    --> src/rm_curation_pipeline.rs:173:5
[INFO] [stdout]     |
[INFO] [stdout] 173 |     minfrac: f64,
[INFO] [stdout]     |     ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_minfrac`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `flank`
[INFO] [stdout]   --> src/rm_curation_pipeline.rs:81:9
[INFO] [stdout]    |
[INFO] [stdout] 81 |     let flank = 2000;
[INFO] [stdout]    |         ^^^^^ help: if this is intentional, prefix it with an underscore: `_flank`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `digits`
[INFO] [stdout]   --> src/rm_curation_pipeline.rs:84:9
[INFO] [stdout]    |
[INFO] [stdout] 84 |     let digits = 5;
[INFO] [stdout]    |         ^^^^^^ help: if this is intentional, prefix it with an underscore: `_digits`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `temp_mafft`
[INFO] [stdout]   --> src/rm_curation_pipeline.rs:99:9
[INFO] [stdout]    |
[INFO] [stdout] 99 |     let temp_mafft = matches.configure.join(INTERMEDIATE).join("tempMafft.txt");
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_temp_mafft`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `rmdl_library_reader`
[INFO] [stdout]    --> src/rm_curation_pipeline.rs:207:9
[INFO] [stdout]     |
[INFO] [stdout] 207 |     let rmdl_library_reader = fasta::Reader::from_file(rmdl_library)?;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_rmdl_library_reader`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `unique_hits`
[INFO] [stdout]    --> src/rm_curation_pipeline.rs:236:13
[INFO] [stdout]     |
[INFO] [stdout] 236 |         let unique_hits = top_blast_hits.filter_unique_combinations();
[INFO] [stdout]     |             ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_unique_hits`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `maxhitdist`
[INFO] [stdout]    --> src/rm_curation_pipeline.rs:172:5
[INFO] [stdout]     |
[INFO] [stdout] 172 |     maxhitdist: i32,
[INFO] [stdout]     |     ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_maxhitdist`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `minfrac`
[INFO] [stdout]    --> src/rm_curation_pipeline.rs:173:5
[INFO] [stdout]     |
[INFO] [stdout] 173 |     minfrac: f64,
[INFO] [stdout]     |     ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_minfrac`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 27.97s
[INFO] running `Command { std: "docker" "inspect" "842027efb2548335023e33ec46904ada5113ebfbf7a1bd133f1473a9809803ac", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "842027efb2548335023e33ec46904ada5113ebfbf7a1bd133f1473a9809803ac", kill_on_drop: false }`
[INFO] [stdout] 842027efb2548335023e33ec46904ada5113ebfbf7a1bd133f1473a9809803ac
