[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] building Dfam-consortium/DisCoord against master#ad85bc524b1ad696e42061ad8338d382dffbdbe5 for pr-146237-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FDfam-consortium%2FDisCoord" "/workspace/builds/worker-6-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-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-6-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/Dfam-consortium/DisCoord on toolchain ad85bc524b1ad696e42061ad8338d382dffbdbe5
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "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" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "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]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded strum v0.20.0
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[INFO] [stderr]   Downloaded triple_accel v0.3.4
[INFO] [stderr]   Downloaded derive-new v0.6.0
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[INFO] [stderr]   Downloaded enum-map v0.6.6
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded semver v0.1.20
[INFO] [stderr]   Downloaded strum_macros v0.20.1
[INFO] [stderr]   Downloaded simba v0.4.0
[INFO] [stderr]   Downloaded anyhow v1.0.92
[INFO] [stderr]   Downloaded statrs v0.14.0
[INFO] [stderr]   Downloaded bio v0.35.0
[INFO] [stderr]   Downloaded ndarray v0.14.0
[INFO] [stderr]   Downloaded nalgebra v0.26.2
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/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" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 11dc0dfaf018a53c16d97b3c5775bd5b969612abda2b743bc83c7e8d1f128883
[INFO] running `Command { std: "docker" "start" "-a" "11dc0dfaf018a53c16d97b3c5775bd5b969612abda2b743bc83c7e8d1f128883", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "11dc0dfaf018a53c16d97b3c5775bd5b969612abda2b743bc83c7e8d1f128883", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "11dc0dfaf018a53c16d97b3c5775bd5b969612abda2b743bc83c7e8d1f128883", kill_on_drop: false }`
[INFO] [stdout] 11dc0dfaf018a53c16d97b3c5775bd5b969612abda2b743bc83c7e8d1f128883
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 2a871f4298a1a6bfcc15577817d84b514edbcaa483f89759bd3242e1a698683a
[INFO] running `Command { std: "docker" "start" "-a" "2a871f4298a1a6bfcc15577817d84b514edbcaa483f89759bd3242e1a698683a", 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 syn v1.0.109
[INFO] [stderr]    Compiling serde v1.0.214
[INFO] [stderr]    Compiling rawpointer v0.2.1
[INFO] [stderr]    Compiling semver v0.1.20
[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 rustversion v1.0.18
[INFO] [stderr]    Compiling regex-automata v0.4.8
[INFO] [stderr]    Compiling indexmap v1.9.3
[INFO] [stderr]    Compiling thiserror v1.0.68
[INFO] [stderr]    Compiling ndarray v0.14.0
[INFO] [stderr]    Compiling anyhow v1.0.92
[INFO] [stderr]    Compiling matrixmultiply v0.2.4
[INFO] [stderr]    Compiling csv-core v0.1.11
[INFO] [stderr]    Compiling bio v0.35.0
[INFO] [stderr]    Compiling array-macro v1.0.5
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling fixedbitset v0.2.0
[INFO] [stderr]    Compiling bit-set v0.5.3
[INFO] [stderr]    Compiling clap_builder v4.5.20
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling miniz_oxide v0.8.0
[INFO] [stderr]    Compiling itertools v0.9.0
[INFO] [stderr]    Compiling fxhash v0.2.1
[INFO] [stderr]    Compiling triple_accel v0.3.4
[INFO] [stderr]    Compiling strum v0.20.0
[INFO] [stderr]    Compiling bytecount v0.6.8
[INFO] [stderr]    Compiling quote v1.0.37
[INFO] [stderr]    Compiling petgraph v0.5.1
[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling syn v2.0.87
[INFO] [stderr]    Compiling flate2 v1.0.34
[INFO] [stderr]    Compiling getrandom v0.2.15
[INFO] [stderr]    Compiling memmap2 v0.9.5
[INFO] [stderr]    Compiling rand_core v0.6.4
[INFO] [stderr]    Compiling num-complex v0.3.1
[INFO] [stderr]    Compiling num-integer v0.1.46
[INFO] [stderr]    Compiling approx v0.4.0
[INFO] [stderr]    Compiling approx v0.3.2
[INFO] [stderr]    Compiling itertools-num v0.1.3
[INFO] [stderr]    Compiling ordered-float v1.1.1
[INFO] [stderr]    Compiling simba v0.4.0
[INFO] [stderr]    Compiling regex v1.11.1
[INFO] [stderr]    Compiling enum-map-derive v0.4.6
[INFO] [stderr]    Compiling strum_macros v0.20.1
[INFO] [stderr]    Compiling getset v0.0.9
[INFO] [stderr]    Compiling smitten v0.1.0 (https://github.com/Dfam-consortium/Smitten.git#1d2faac3)
[INFO] [stderr]    Compiling 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 derive-new v0.6.0
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling clap_derive v4.5.18
[INFO] [stderr]    Compiling zerocopy v0.7.35
[INFO] [stderr]    Compiling ppv-lite86 v0.2.20
[INFO] [stderr]    Compiling bio-types v1.0.4
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling rand v0.8.5
[INFO] [stderr]    Compiling clap v4.5.20
[INFO] [stderr]    Compiling rand_distr v0.4.3
[INFO] [stderr]    Compiling nalgebra v0.26.2
[INFO] [stderr]    Compiling csv v1.3.0
[INFO] [stderr]    Compiling multimap v0.8.3
[INFO] [stderr]    Compiling vec_map v0.8.2
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]    Compiling statrs v0.14.0
[INFO] [stderr]    Compiling 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 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: bool, ...
[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 1m 06s
[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 4`
[INFO] running `Command { std: "docker" "inspect" "2a871f4298a1a6bfcc15577817d84b514edbcaa483f89759bd3242e1a698683a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "2a871f4298a1a6bfcc15577817d84b514edbcaa483f89759bd3242e1a698683a", kill_on_drop: false }`
[INFO] [stdout] 2a871f4298a1a6bfcc15577817d84b514edbcaa483f89759bd3242e1a698683a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] b48cb9bc45c009cf532c56d0998509ae0df13f896ab1977235e0d53e3cf34a45
[INFO] running `Command { std: "docker" "start" "-a" "b48cb9bc45c009cf532c56d0998509ae0df13f896ab1977235e0d53e3cf34a45", kill_on_drop: false }`
[INFO] [stderr]    Compiling 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 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: bool, ...
[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 `test` profile [unoptimized + debuginfo] target(s) in 0.88s
[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 4`
[INFO] running `Command { std: "docker" "inspect" "b48cb9bc45c009cf532c56d0998509ae0df13f896ab1977235e0d53e3cf34a45", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "b48cb9bc45c009cf532c56d0998509ae0df13f896ab1977235e0d53e3cf34a45", kill_on_drop: false }`
[INFO] [stdout] b48cb9bc45c009cf532c56d0998509ae0df13f896ab1977235e0d53e3cf34a45
