[INFO] cloning repository https://github.com/ncsa/rusty-neat [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/ncsa/rusty-neat" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fncsa%2Frusty-neat", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fncsa%2Frusty-neat'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 79389bfd5eee4dd62e36b0395ba6a78a91e53d33 [INFO] checking ncsa/rusty-neat against master#336209eef13882bd1e211b24779584cb7ef911eb for pr-129249 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fncsa%2Frusty-neat" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/ncsa/rusty-neat on toolchain 336209eef13882bd1e211b24779584cb7ef911eb [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+336209eef13882bd1e211b24779584cb7ef911eb" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/ncsa/rusty-neat [INFO] finished tweaking git repo https://github.com/ncsa/rusty-neat [INFO] tweaked toml for git repo https://github.com/ncsa/rusty-neat written to /workspace/builds/worker-5-tc1/source/Cargo.toml [INFO] crate git repo https://github.com/ncsa/rusty-neat 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" "+336209eef13882bd1e211b24779584cb7ef911eb" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded xorshift v0.1.3 [INFO] [stderr] Downloaded nalgebra-macros v0.2.2 [INFO] [stderr] Downloaded simplelog v0.12.2 [INFO] [stderr] Downloaded cc v1.1.37 [INFO] [stderr] Downloaded bytemuck v1.19.0 [INFO] [stderr] Downloaded statrs v0.17.1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:f3a9d4ad9d972b27faf3965f35b62e55ba32bbce8f20bc8fe909558a86702fde" "/opt/rustwide/cargo-home/bin/cargo" "+336209eef13882bd1e211b24779584cb7ef911eb" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 296fe60b459dcafd52077272908d0e9157254ef3bbaf6494d26007e6cbfd6487 [INFO] running `Command { std: "docker" "start" "-a" "296fe60b459dcafd52077272908d0e9157254ef3bbaf6494d26007e6cbfd6487", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "296fe60b459dcafd52077272908d0e9157254ef3bbaf6494d26007e6cbfd6487", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "296fe60b459dcafd52077272908d0e9157254ef3bbaf6494d26007e6cbfd6487", kill_on_drop: false }` [INFO] [stdout] 296fe60b459dcafd52077272908d0e9157254ef3bbaf6494d26007e6cbfd6487 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:f3a9d4ad9d972b27faf3965f35b62e55ba32bbce8f20bc8fe909558a86702fde" "/opt/rustwide/cargo-home/bin/cargo" "+336209eef13882bd1e211b24779584cb7ef911eb" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] ea359cdd62d90ae8d75e70d89839e4dfc3132bd4b51ccfb16b273f8ad671c986 [INFO] running `Command { std: "docker" "start" "-a" "ea359cdd62d90ae8d75e70d89839e4dfc3132bd4b51ccfb16b273f8ad671c986", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.89 [INFO] [stderr] Compiling libc v0.2.162 [INFO] [stderr] Compiling libm v0.2.11 [INFO] [stderr] Compiling crossbeam-utils v0.8.20 [INFO] [stderr] Checking bytemuck v1.19.0 [INFO] [stderr] Checking regex-syntax v0.8.5 [INFO] [stderr] Checking anstyle v1.0.10 [INFO] [stderr] Checking log v0.4.22 [INFO] [stderr] Checking bitflags v2.6.0 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Checking aho-corasick v1.1.3 [INFO] [stderr] Compiling matrixmultiply v0.3.9 [INFO] [stderr] Checking bstr v1.10.0 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Checking same-file v1.0.6 [INFO] [stderr] Compiling serde v1.0.214 [INFO] [stderr] Compiling rustix v0.38.39 [INFO] [stderr] Checking utf8parse v0.2.2 [INFO] [stderr] Checking walkdir v2.5.0 [INFO] [stderr] Checking is_terminal_polyfill v1.70.1 [INFO] [stderr] Checking anstyle-parse v0.2.6 [INFO] [stderr] Checking colorchoice v1.0.3 [INFO] [stderr] Compiling doc-comment v0.3.3 [INFO] [stderr] Checking linux-raw-sys v0.4.14 [INFO] [stderr] Checking anstyle-query v1.1.2 [INFO] [stderr] Checking safe_arch v0.7.2 [INFO] [stderr] Checking predicates-core v1.0.8 [INFO] [stderr] Compiling time-macros v0.2.18 [INFO] [stderr] Checking fastrand v2.2.0 [INFO] [stderr] Checking difflib v0.4.0 [INFO] [stderr] Checking termtree v0.4.1 [INFO] [stderr] Checking anstream v0.6.18 [INFO] [stderr] Checking hashbrown v0.15.1 [INFO] [stderr] Compiling serde_json v1.0.132 [INFO] [stderr] Checking num_threads v0.1.7 [INFO] [stderr] Checking once_cell v1.20.2 [INFO] [stderr] Checking clap_lex v0.7.2 [INFO] [stderr] Checking predicates-tree v1.0.11 [INFO] [stderr] Checking unsafe-libyaml v0.2.11 [INFO] [stderr] Checking either v1.13.0 [INFO] [stderr] Checking termcolor v1.4.1 [INFO] [stderr] Checking lazy_static v0.2.11 [INFO] [stderr] Checking predicates v3.1.2 [INFO] [stderr] Checking clap_builder v4.5.20 [INFO] [stderr] Checking wide v0.7.28 [INFO] [stderr] Compiling quote v1.0.37 [INFO] [stderr] Checking itertools v0.12.1 [INFO] [stderr] Checking crossbeam-epoch v0.9.18 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Checking num-complex v0.4.6 [INFO] [stderr] Checking chrono v0.4.38 [INFO] [stderr] Checking indexmap v2.6.0 [INFO] [stderr] Checking regex-automata v0.4.8 [INFO] [stderr] Compiling syn v2.0.87 [INFO] [stderr] Checking num-rational v0.4.2 [INFO] [stderr] Checking getrandom v0.2.15 [INFO] [stderr] Checking rand v0.4.6 [INFO] [stderr] Checking crossbeam-deque v0.8.5 [INFO] [stderr] Checking rand_core v0.6.4 [INFO] [stderr] Checking time v0.3.36 [INFO] [stderr] Checking rand v0.3.23 [INFO] [stderr] Checking xorshift v0.1.3 [INFO] [stderr] Checking tempfile v3.14.0 [INFO] [stderr] Checking simba v0.8.1 [INFO] [stderr] Checking simplelog v0.12.2 [INFO] [stderr] Checking globset v0.4.15 [INFO] [stderr] Checking ignore v0.4.23 [INFO] [stderr] Checking globwalk v0.9.1 [INFO] [stderr] Checking assert_fs v1.1.2 [INFO] [stderr] Compiling zerocopy-derive v0.7.35 [INFO] [stderr] Compiling nalgebra-macros v0.2.2 [INFO] [stderr] Compiling serde_derive v1.0.214 [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 rand v0.8.5 [INFO] [stderr] Checking clap v4.5.20 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking nalgebra v0.32.6 [INFO] [stderr] Checking serde_yaml v0.9.34+deprecated [INFO] [stderr] Checking statrs v0.17.1 [INFO] [stderr] Checking simple_rng v0.1.0 (/opt/rustwide/workdir/simple_rng) [INFO] [stderr] Checking rusty-neat v0.2.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `std::error` [INFO] [stdout] --> src/utils/fasta_tools.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::error; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs` [INFO] [stdout] --> src/utils/fasta_tools.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use std::fs; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `mutation_rate` and `produce_bam` are never read [INFO] [stdout] --> src/utils/config.rs:42:9 [INFO] [stdout] | [INFO] [stdout] 15 | pub struct RunConfiguration { [INFO] [stdout] | ---------------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 42 | pub mutation_rate: f64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 50 | pub produce_bam: bool, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `RunConfiguration` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `display`, `display_it_all`, and `write_out_quality_model` are never used [INFO] [stdout] --> src/utils/quality_scores.rs:67:12 [INFO] [stdout] | [INFO] [stdout] 65 | impl QualityScoreModel { [INFO] [stdout] | ---------------------- associated items in this implementation [INFO] [stdout] 66 | // methods for QualityScoreModel objects [INFO] [stdout] 67 | pub fn new() -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 99 | pub fn display(&self) -> String { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 113 | pub fn display_it_all(&self) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 210 | pub fn write_out_quality_model(&self, filename: &mut str) -> serde_json::Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `convert_to_weights` is never used [INFO] [stdout] --> src/utils/read_old_data.rs:13:8 [INFO] [stdout] | [INFO] [stdout] 12 | impl QualityRaw { [INFO] [stdout] | --------------- method in this implementation [INFO] [stdout] 13 | fn convert_to_weights(&self) -> QualityScoreModel { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_neat_quality_scores` is never used [INFO] [stdout] --> src/utils/read_old_data.rs:46:8 [INFO] [stdout] | [INFO] [stdout] 46 | pub fn parse_neat_quality_scores(filename: &str) -> QualityScoreModel { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 30.24s [INFO] running `Command { std: "docker" "inspect" "ea359cdd62d90ae8d75e70d89839e4dfc3132bd4b51ccfb16b273f8ad671c986", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "ea359cdd62d90ae8d75e70d89839e4dfc3132bd4b51ccfb16b273f8ad671c986", kill_on_drop: false }` [INFO] [stdout] ea359cdd62d90ae8d75e70d89839e4dfc3132bd4b51ccfb16b273f8ad671c986