[INFO] cloning repository https://github.com/Dfam-consortium/DisCoord
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/Dfam-consortium/DisCoord" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FDfam-consortium%2FDisCoord", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FDfam-consortium%2FDisCoord'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 698dd685de98f7d2e0f406416ae05f60c86447d3
[INFO] checking Dfam-consortium/DisCoord against master#4eb62535fc12dd1a63fd43a4173e224e79313c4d for pr-158816
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FDfam-consortium%2FDisCoord" "/workspace/builds/worker-4-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-4-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/Dfam-consortium/DisCoord
[INFO] finished tweaking git repo https://github.com/Dfam-consortium/DisCoord
[INFO] tweaked toml for git repo https://github.com/Dfam-consortium/DisCoord written to /workspace/builds/worker-4-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/Dfam-consortium/DisCoord on toolchain 4eb62535fc12dd1a63fd43a4173e224e79313c4d
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+4eb62535fc12dd1a63fd43a4173e224e79313c4d" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/Dfam-consortium/DisCoord 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" "+4eb62535fc12dd1a63fd43a4173e224e79313c4d" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Updating git repository `https://github.com/Dfam-consortium/Smitten.git`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded serde v1.0.214
[INFO] [stderr]   Downloaded clap v4.5.20
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded enum-map-derive v0.4.6
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[INFO] [stderr]   Downloaded enum-map v0.6.6
[INFO] [stderr]   Downloaded num-complex v0.3.1
[INFO] [stderr]   Downloaded array-macro v1.0.5
[INFO] [stderr]   Downloaded derive-new v0.6.0
[INFO] [stderr]   Downloaded getset v0.0.9
[INFO] [stderr]   Downloaded thiserror-impl v1.0.68
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[INFO] [stderr]   Downloaded bytecount v0.6.8
[INFO] [stderr]   Downloaded serde_derive v1.0.214
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[INFO] [stderr]   Downloaded matrixmultiply v0.2.4
[INFO] [stderr]   Downloaded clap_builder v4.5.20
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[INFO] [stderr]   Downloaded bio v0.35.0
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[INFO] [stderr]   Downloaded nalgebra v0.26.2
[INFO] [stderr]   Downloaded libc v0.2.161
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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@sha256:3d5ced03c013a94a2f102a4510f48a6e9184255caf5fd8244f58017bde7f5210" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 64672a17de2bb02ab2c9a669352906e4273a86908087887db792d662cbee8ded
[INFO] running `Command { std: "docker" "start" "64672a17de2bb02ab2c9a669352906e4273a86908087887db792d662cbee8ded", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "64672a17de2bb02ab2c9a669352906e4273a86908087887db792d662cbee8ded", 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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "64672a17de2bb02ab2c9a669352906e4273a86908087887db792d662cbee8ded" "/opt/rustwide/cargo-home/bin/cargo" "+4eb62535fc12dd1a63fd43a4173e224e79313c4d" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "64672a17de2bb02ab2c9a669352906e4273a86908087887db792d662cbee8ded", 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=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-w" "/opt/rustwide/workdir" "--user" "0:0" "64672a17de2bb02ab2c9a669352906e4273a86908087887db792d662cbee8ded" "/opt/rustwide/cargo-home/bin/cargo" "+4eb62535fc12dd1a63fd43a4173e224e79313c4d" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.89
[INFO] [stderr]    Compiling unicode-ident v1.0.13
[INFO] [stderr]    Compiling libm v0.2.11
[INFO] [stderr]    Compiling libc v0.2.161
[INFO] [stderr]    Compiling serde v1.0.214
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling crossbeam-utils v0.8.20
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling matrixmultiply v0.3.9
[INFO] [stderr]    Compiling num-rational v0.3.2
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]     Checking regex-automata v0.4.8
[INFO] [stderr]    Compiling indexmap v1.9.3
[INFO] [stderr]    Compiling thiserror v1.0.68
[INFO] [stderr]    Compiling anyhow v1.0.92
[INFO] [stderr]     Checking either v1.13.0
[INFO] [stderr]    Compiling ndarray v0.14.0
[INFO] [stderr]     Checking matrixmultiply v0.2.4
[INFO] [stderr]     Checking csv-core v0.1.11
[INFO] [stderr]     Checking clap_lex v0.7.2
[INFO] [stderr]     Checking fixedbitset v0.2.0
[INFO] [stderr]     Checking bit-vec v0.6.3
[INFO] [stderr]     Checking array-macro v1.0.5
[INFO] [stderr]    Compiling bio v0.35.0
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking clap_builder v4.5.20
[INFO] [stderr]     Checking miniz_oxide v0.8.0
[INFO] [stderr]     Checking itertools v0.9.0
[INFO] [stderr]     Checking bit-set v0.5.3
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking triple_accel v0.3.4
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking bytecount v0.6.8
[INFO] [stderr]     Checking strum v0.20.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking crossbeam-epoch v0.9.18
[INFO] [stderr]     Checking petgraph v0.5.1
[INFO] [stderr]    Compiling quote v1.0.37
[INFO] [stderr]     Checking flate2 v1.0.34
[INFO] [stderr]     Checking crossbeam-deque v0.8.5
[INFO] [stderr]     Checking getrandom v0.2.15
[INFO] [stderr]     Checking memmap2 v0.9.5
[INFO] [stderr]     Checking rayon-core v1.12.1
[INFO] [stderr]    Compiling syn v2.0.87
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking rayon v1.10.0
[INFO] [stderr]     Checking num-complex v0.3.1
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking approx v0.4.0
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v1.1.1
[INFO] [stderr]     Checking approx v0.3.2
[INFO] [stderr]     Checking simba v0.4.0
[INFO] [stderr]     Checking regex v1.11.1
[INFO] [stderr]     Checking smitten v0.1.0 (https://github.com/Dfam-consortium/Smitten.git#1d2faac3)
[INFO] [stderr]    Compiling enum-map-derive v0.4.6
[INFO] [stderr]    Compiling getset v0.0.9
[INFO] [stderr]    Compiling strum_macros v0.20.1
[INFO] [stderr]     Checking enum-map v0.6.6
[INFO] [stderr]    Compiling zerocopy-derive v0.7.35
[INFO] [stderr]    Compiling serde_derive v1.0.214
[INFO] [stderr]    Compiling thiserror-impl v1.0.68
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling clap_derive v4.5.18
[INFO] [stderr]     Checking zerocopy v0.7.35
[INFO] [stderr]     Checking ppv-lite86 v0.2.20
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking clap v4.5.20
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking nalgebra v0.26.2
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking csv v1.3.0
[INFO] [stderr]     Checking multimap v0.8.3
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking statrs v0.14.0
[INFO] [stderr]     Checking DisCoord v0.3.3 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `std::fs`
[INFO] [stdout]   --> src/main.rs:20:5
[INFO] [stdout]    |
[INFO] [stdout] 20 | use std::fs;
[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`
[INFO] [stdout]   --> src/main.rs:20:5
[INFO] [stdout]    |
[INFO] [stdout] 20 | use std::fs;
[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 variable: `label`
[INFO] [stdout]    --> src/main.rs:225:17
[INFO] [stdout]     |
[INFO] [stdout] 225 |             let label = if !accession.is_empty() {
[INFO] [stdout]     |                 ^^^^^ help: if this is intentional, prefix it with an underscore: `_label`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_and_validate_stockholm_old` is never used
[INFO] [stdout]   --> src/main.rs:93:4
[INFO] [stdout]    |
[INFO] [stdout] 93 | fn parse_and_validate_stockholm_old(file_path: &str, genome_map: &HashMap<String, Vec<u8>>, output_path: &Option<String>, is_gzip: b...
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `process_stockholm_record_old` is never used
[INFO] [stdout]    --> src/main.rs:360:4
[INFO] [stdout]     |
[INFO] [stdout] 360 | fn process_stockholm_record_old(
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `label`
[INFO] [stdout]    --> src/main.rs:225:17
[INFO] [stdout]     |
[INFO] [stdout] 225 |             let label = if !accession.is_empty() {
[INFO] [stdout]     |                 ^^^^^ help: if this is intentional, prefix it with an underscore: `_label`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_and_validate_stockholm_old` is never used
[INFO] [stdout]   --> src/main.rs:93:4
[INFO] [stdout]    |
[INFO] [stdout] 93 | fn parse_and_validate_stockholm_old(file_path: &str, genome_map: &HashMap<String, Vec<u8>>, output_path: &Option<String>, is_gzip: b...
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `process_stockholm_record_old` is never used
[INFO] [stdout]    --> src/main.rs:360:4
[INFO] [stdout]     |
[INFO] [stdout] 360 | fn process_stockholm_record_old(
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 34.51s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.26.2
[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" "64672a17de2bb02ab2c9a669352906e4273a86908087887db792d662cbee8ded", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "64672a17de2bb02ab2c9a669352906e4273a86908087887db792d662cbee8ded", kill_on_drop: false }`
[INFO] [stdout] 64672a17de2bb02ab2c9a669352906e4273a86908087887db792d662cbee8ded
