[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] e30e7983023d731941a38626ab084081de643854 [INFO] checking ncsa/rusty-neat against master#385fa9d845dd326c6bbfd58c22244215e431948a for absurd-question-mark-desugar [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fncsa%2Frusty-neat" "/workspace/builds/worker-3-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc1/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/ncsa/rusty-neat on toolchain 385fa9d845dd326c6bbfd58c22244215e431948a [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+385fa9d845dd326c6bbfd58c22244215e431948a" "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-3-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" "+385fa9d845dd326c6bbfd58c22244215e431948a" "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 rand_chacha v0.9.0-alpha.1 [INFO] [stderr] Downloaded rand_core v0.9.0-alpha.1 [INFO] [stderr] Downloaded zerocopy-derive v0.8.0-alpha.6 [INFO] [stderr] Downloaded zerocopy v0.8.0-alpha.6 [INFO] [stderr] Downloaded rand v0.9.0-alpha.1 [INFO] [stderr] Downloaded rand_distr v0.5.0-alpha.1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+385fa9d845dd326c6bbfd58c22244215e431948a" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 7f20eb20a5ca8679d1029b79e366f551d0ad6c1efe06ce55a391ff58ef6fb57f [INFO] running `Command { std: "docker" "start" "-a" "7f20eb20a5ca8679d1029b79e366f551d0ad6c1efe06ce55a391ff58ef6fb57f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "7f20eb20a5ca8679d1029b79e366f551d0ad6c1efe06ce55a391ff58ef6fb57f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "7f20eb20a5ca8679d1029b79e366f551d0ad6c1efe06ce55a391ff58ef6fb57f", kill_on_drop: false }` [INFO] [stdout] 7f20eb20a5ca8679d1029b79e366f551d0ad6c1efe06ce55a391ff58ef6fb57f [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+385fa9d845dd326c6bbfd58c22244215e431948a" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 65451383f7eff02494eeeea4fa72762863805a205b46d0b449ef94fbb5ef035e [INFO] running `Command { std: "docker" "start" "-a" "65451383f7eff02494eeeea4fa72762863805a205b46d0b449ef94fbb5ef035e", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.153 [INFO] [stderr] Compiling proc-macro2 v1.0.78 [INFO] [stderr] Compiling unicode-ident v1.0.12 [INFO] [stderr] Compiling crossbeam-utils v0.8.19 [INFO] [stderr] Checking memchr v2.7.1 [INFO] [stderr] Compiling zerocopy v0.8.0-alpha.6 [INFO] [stderr] Compiling libm v0.2.8 [INFO] [stderr] Checking anstyle v1.0.6 [INFO] [stderr] Checking log v0.4.21 [INFO] [stderr] Checking regex-syntax v0.8.2 [INFO] [stderr] Compiling num-traits v0.2.18 [INFO] [stderr] Compiling rustix v0.38.31 [INFO] [stderr] Checking aho-corasick v1.1.2 [INFO] [stderr] Checking bstr v1.9.1 [INFO] [stderr] Checking crossbeam-epoch v0.9.18 [INFO] [stderr] Compiling serde v1.0.197 [INFO] [stderr] Compiling quote v1.0.35 [INFO] [stderr] Checking bitflags v2.4.2 [INFO] [stderr] Checking itoa v1.0.10 [INFO] [stderr] Checking utf8parse v0.2.1 [INFO] [stderr] Checking crossbeam-deque v0.8.5 [INFO] [stderr] Compiling syn v2.0.52 [INFO] [stderr] Checking anstyle-parse v0.2.3 [INFO] [stderr] Checking linux-raw-sys v0.4.13 [INFO] [stderr] Checking colorchoice v1.0.0 [INFO] [stderr] Checking predicates-core v1.0.6 [INFO] [stderr] Compiling doc-comment v0.3.3 [INFO] [stderr] Compiling time-core v0.1.2 [INFO] [stderr] Checking regex-automata v0.4.6 [INFO] [stderr] Checking powerfmt v0.2.0 [INFO] [stderr] Compiling num-conv v0.1.0 [INFO] [stderr] Checking anstyle-query v1.0.2 [INFO] [stderr] Checking deranged v0.3.11 [INFO] [stderr] Checking anstream v0.6.13 [INFO] [stderr] Compiling time-macros v0.2.17 [INFO] [stderr] Checking hashbrown v0.14.3 [INFO] [stderr] Checking getrandom v0.2.12 [INFO] [stderr] Checking rand_core v0.9.0-alpha.1 [INFO] [stderr] Checking rand_chacha v0.9.0-alpha.1 [INFO] [stderr] Checking rand v0.4.6 [INFO] [stderr] Checking clap_lex v0.7.0 [INFO] [stderr] Checking ryu v1.0.17 [INFO] [stderr] Checking num_threads v0.1.7 [INFO] [stderr] Compiling heck v0.4.1 [INFO] [stderr] Checking termtree v0.4.1 [INFO] [stderr] Checking equivalent v1.0.1 [INFO] [stderr] Checking strsim v0.11.0 [INFO] [stderr] Checking fastrand v2.0.1 [INFO] [stderr] Compiling serde_json v1.0.114 [INFO] [stderr] Checking difflib v0.4.0 [INFO] [stderr] Checking clap_builder v4.5.1 [INFO] [stderr] Checking rand v0.3.23 [INFO] [stderr] Checking indexmap v2.2.5 [INFO] [stderr] Checking predicates v3.1.0 [INFO] [stderr] Checking predicates-tree v1.0.9 [INFO] [stderr] Checking rand v0.9.0-alpha.1 [INFO] [stderr] Checking iana-time-zone v0.1.60 [INFO] [stderr] Checking unsafe-libyaml v0.2.10 [INFO] [stderr] Checking lazy_static v0.2.11 [INFO] [stderr] Checking tempfile v3.10.1 [INFO] [stderr] Checking either v1.10.0 [INFO] [stderr] Checking globset v0.4.14 [INFO] [stderr] Checking xorshift v0.1.3 [INFO] [stderr] Checking rand_distr v0.5.0-alpha.1 [INFO] [stderr] Checking itertools v0.12.1 [INFO] [stderr] Checking chrono v0.4.34 [INFO] [stderr] Checking time v0.3.34 [INFO] [stderr] Checking ignore v0.4.22 [INFO] [stderr] Checking globwalk v0.9.1 [INFO] [stderr] Checking assert_fs v1.1.1 [INFO] [stderr] Checking simplelog v0.12.1 [INFO] [stderr] Compiling serde_derive v1.0.197 [INFO] [stderr] Compiling clap_derive v4.5.0 [INFO] [stderr] Checking clap v4.5.1 [INFO] [stderr] Checking serde_yaml v0.9.32 [INFO] [stderr] Checking rusty-neat v0.2.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: the item `io` is imported redundantly [INFO] [stdout] --> src/utils/fasta_tools.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::io; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 5 | use std::io::Write; [INFO] [stdout] 6 | use std::*; [INFO] [stdout] | ------ the item `io` is already imported here [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `String` is imported redundantly [INFO] [stdout] --> src/utils/config.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::string::String; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] --> /rustc/385fa9d845dd326c6bbfd58c22244215e431948a/library/std/src/prelude/mod.rs:124:13 [INFO] [stdout] | [INFO] [stdout] = note: the item `String` is already defined here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `Rng` is imported redundantly [INFO] [stdout] --> src/utils/mutate.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 8 | use rand::prelude::*; [INFO] [stdout] | ---------------- the item `Rng` is already imported here [INFO] [stdout] 9 | use rand::Rng; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `serde_json` is imported redundantly [INFO] [stdout] --> src/utils/read_models.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use serde_json; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] ::: src/main.rs:10:1 [INFO] [stdout] | [INFO] [stdout] 10 | extern crate serde_json; [INFO] [stdout] | ------------------------ the item `serde_json` is already imported here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `io` is imported redundantly [INFO] [stdout] --> src/utils/fasta_tools.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::io; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 5 | use std::io::Write; [INFO] [stdout] 6 | use std::*; [INFO] [stdout] | ------ the item `io` is already imported here [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `NeatRng` is imported redundantly [INFO] [stdout] --> src/utils/make_reads.rs:157:9 [INFO] [stdout] | [INFO] [stdout] 155 | use super::*; [INFO] [stdout] | -------- the item `NeatRng` is already imported here [INFO] [stdout] 156 | use rand::SeedableRng; [INFO] [stdout] 157 | use utils::neat_rng::NeatRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `Rng` is imported redundantly [INFO] [stdout] --> src/utils/mutate.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 8 | use rand::prelude::*; [INFO] [stdout] | ---------------- the item `Rng` is already imported here [INFO] [stdout] 9 | use rand::Rng; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `SeedableRng` is imported redundantly [INFO] [stdout] --> src/utils/mutate.rs:146:9 [INFO] [stdout] | [INFO] [stdout] 146 | use rand::SeedableRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] 147 | use utils::neat_rng::NeatRng; [INFO] [stdout] 148 | use super::*; [INFO] [stdout] | -------- the item `SeedableRng` is already imported here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `NeatRng` is imported redundantly [INFO] [stdout] --> src/utils/mutate.rs:147:9 [INFO] [stdout] | [INFO] [stdout] 147 | use utils::neat_rng::NeatRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 148 | use super::*; [INFO] [stdout] | -------- the item `NeatRng` is already imported here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `NeatRng` is imported redundantly [INFO] [stdout] --> src/utils/vcf_tools.rs:111:9 [INFO] [stdout] | [INFO] [stdout] 109 | use super::*; [INFO] [stdout] | -------- the item `NeatRng` is already imported here [INFO] [stdout] 110 | use std::path::Path; [INFO] [stdout] 111 | use utils::neat_rng::NeatRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `RngCore` is imported redundantly [INFO] [stdout] --> src/utils/neat_rng.rs:82:16 [INFO] [stdout] | [INFO] [stdout] 81 | use super::*; [INFO] [stdout] | -------- the item `RngCore` is already imported here [INFO] [stdout] 82 | use rand::{RngCore, SeedableRng}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `SeedableRng` is imported redundantly [INFO] [stdout] --> src/utils/neat_rng.rs:82:25 [INFO] [stdout] | [INFO] [stdout] 81 | use super::*; [INFO] [stdout] | -------- the item `SeedableRng` is already imported here [INFO] [stdout] 82 | use rand::{RngCore, SeedableRng}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `serde_json` is imported redundantly [INFO] [stdout] --> src/utils/read_models.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use serde_json; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] ::: src/main.rs:10:1 [INFO] [stdout] | [INFO] [stdout] 10 | extern crate serde_json; [INFO] [stdout] | ------------------------ the item `serde_json` is already imported here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `mutation_rate` and `produce_bam` are never read [INFO] [stdout] --> src/utils/config.rs:43:9 [INFO] [stdout] | [INFO] [stdout] 16 | pub struct RunConfiguration { [INFO] [stdout] | ---------------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 43 | pub mutation_rate: f64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 51 | 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:69:12 [INFO] [stdout] | [INFO] [stdout] 67 | impl QualityScoreModel { [INFO] [stdout] | ---------------------- associated items in this implementation [INFO] [stdout] 68 | // methods for QualityScoreModel objects [INFO] [stdout] 69 | pub fn new() -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 101 | pub fn display(&self) -> String { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 115 | pub fn display_it_all(&self) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 212 | 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] [stdout] warning: 8 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 9 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 44.37s [INFO] running `Command { std: "docker" "inspect" "65451383f7eff02494eeeea4fa72762863805a205b46d0b449ef94fbb5ef035e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "65451383f7eff02494eeeea4fa72762863805a205b46d0b449ef94fbb5ef035e", kill_on_drop: false }` [INFO] [stdout] 65451383f7eff02494eeeea4fa72762863805a205b46d0b449ef94fbb5ef035e [INFO] checking ncsa/rusty-neat against try#645bb72776a6a56a1a8f52631a44bd082b2ba509 for absurd-question-mark-desugar [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fncsa%2Frusty-neat" "/workspace/builds/worker-3-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc2/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/ncsa/rusty-neat on toolchain 645bb72776a6a56a1a8f52631a44bd082b2ba509 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+645bb72776a6a56a1a8f52631a44bd082b2ba509" "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-3-tc2/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" "+645bb72776a6a56a1a8f52631a44bd082b2ba509" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+645bb72776a6a56a1a8f52631a44bd082b2ba509" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 0b48a7fc0dd6361d7f9865ebbf65e9e7ad9b7e671c69e25fad0590aa18416d34 [INFO] running `Command { std: "docker" "start" "-a" "0b48a7fc0dd6361d7f9865ebbf65e9e7ad9b7e671c69e25fad0590aa18416d34", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "0b48a7fc0dd6361d7f9865ebbf65e9e7ad9b7e671c69e25fad0590aa18416d34", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "0b48a7fc0dd6361d7f9865ebbf65e9e7ad9b7e671c69e25fad0590aa18416d34", kill_on_drop: false }` [INFO] [stdout] 0b48a7fc0dd6361d7f9865ebbf65e9e7ad9b7e671c69e25fad0590aa18416d34 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+645bb72776a6a56a1a8f52631a44bd082b2ba509" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] f98ad12f3ffe22716b3f4f4bc3a1841c596aaeafc81b77b300975119ff1a7005 [INFO] running `Command { std: "docker" "start" "-a" "f98ad12f3ffe22716b3f4f4bc3a1841c596aaeafc81b77b300975119ff1a7005", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.153 [INFO] [stderr] Compiling proc-macro2 v1.0.78 [INFO] [stderr] Compiling unicode-ident v1.0.12 [INFO] [stderr] Checking memchr v2.7.1 [INFO] [stderr] Compiling crossbeam-utils v0.8.19 [INFO] [stderr] Compiling zerocopy v0.8.0-alpha.6 [INFO] [stderr] Checking anstyle v1.0.6 [INFO] [stderr] Compiling libm v0.2.8 [INFO] [stderr] Checking log v0.4.21 [INFO] [stderr] Checking regex-syntax v0.8.2 [INFO] [stderr] Compiling num-traits v0.2.18 [INFO] [stderr] Checking bitflags v2.4.2 [INFO] [stderr] Checking itoa v1.0.10 [INFO] [stderr] Compiling serde v1.0.197 [INFO] [stderr] Compiling rustix v0.38.31 [INFO] [stderr] Checking crossbeam-epoch v0.9.18 [INFO] [stderr] Checking aho-corasick v1.1.2 [INFO] [stderr] Checking bstr v1.9.1 [INFO] [stderr] Checking utf8parse v0.2.1 [INFO] [stderr] Compiling quote v1.0.35 [INFO] [stderr] Checking anstyle-parse v0.2.3 [INFO] [stderr] Compiling syn v2.0.52 [INFO] [stderr] Checking crossbeam-deque v0.8.5 [INFO] [stderr] Checking powerfmt v0.2.0 [INFO] [stderr] Checking predicates-core v1.0.6 [INFO] [stderr] Checking linux-raw-sys v0.4.13 [INFO] [stderr] Checking colorchoice v1.0.0 [INFO] [stderr] Compiling doc-comment v0.3.3 [INFO] [stderr] Compiling time-core v0.1.2 [INFO] [stderr] Checking anstyle-query v1.0.2 [INFO] [stderr] Compiling num-conv v0.1.0 [INFO] [stderr] Checking anstream v0.6.13 [INFO] [stderr] Compiling time-macros v0.2.17 [INFO] [stderr] Checking getrandom v0.2.12 [INFO] [stderr] Checking rand v0.4.6 [INFO] [stderr] Checking regex-automata v0.4.6 [INFO] [stderr] Checking deranged v0.3.11 [INFO] [stderr] Checking rand_core v0.9.0-alpha.1 [INFO] [stderr] Checking rand_chacha v0.9.0-alpha.1 [INFO] [stderr] Checking fastrand v2.0.1 [INFO] [stderr] Compiling heck v0.4.1 [INFO] [stderr] Checking equivalent v1.0.1 [INFO] [stderr] Checking strsim v0.11.0 [INFO] [stderr] Checking clap_lex v0.7.0 [INFO] [stderr] Checking termtree v0.4.1 [INFO] [stderr] Checking ryu v1.0.17 [INFO] [stderr] Checking hashbrown v0.14.3 [INFO] [stderr] Checking difflib v0.4.0 [INFO] [stderr] Checking num_threads v0.1.7 [INFO] [stderr] Compiling serde_json v1.0.114 [INFO] [stderr] Checking clap_builder v4.5.1 [INFO] [stderr] Checking predicates v3.1.0 [INFO] [stderr] Checking predicates-tree v1.0.9 [INFO] [stderr] Checking rand v0.3.23 [INFO] [stderr] Checking rand v0.9.0-alpha.1 [INFO] [stderr] Checking unsafe-libyaml v0.2.10 [INFO] [stderr] Checking indexmap v2.2.5 [INFO] [stderr] Checking either v1.10.0 [INFO] [stderr] Checking time v0.3.34 [INFO] [stderr] Checking termcolor v1.1.3 [INFO] [stderr] Checking globset v0.4.14 [INFO] [stderr] Checking lazy_static v0.2.11 [INFO] [stderr] Checking tempfile v3.10.1 [INFO] [stderr] Checking iana-time-zone v0.1.60 [INFO] [stderr] Checking xorshift v0.1.3 [INFO] [stderr] Checking itertools v0.12.1 [INFO] [stderr] Checking chrono v0.4.34 [INFO] [stderr] Checking rand_distr v0.5.0-alpha.1 [INFO] [stderr] Checking ignore v0.4.22 [INFO] [stderr] Checking globwalk v0.9.1 [INFO] [stderr] Checking simplelog v0.12.1 [INFO] [stderr] Checking assert_fs v1.1.1 [INFO] [stderr] Compiling serde_derive v1.0.197 [INFO] [stderr] Compiling clap_derive v4.5.0 [INFO] [stderr] Checking clap v4.5.1 [INFO] [stderr] Checking serde_yaml v0.9.32 [INFO] [stderr] Checking rusty-neat v0.2.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: the item `io` is imported redundantly [INFO] [stdout] --> src/utils/fasta_tools.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::io; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 5 | use std::io::Write; [INFO] [stdout] 6 | use std::*; [INFO] [stdout] | ------ the item `io` is already imported here [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `String` is imported redundantly [INFO] [stdout] --> src/utils/config.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::string::String; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] --> /rustc/645bb72776a6a56a1a8f52631a44bd082b2ba509/library/std/src/prelude/mod.rs:124:13 [INFO] [stdout] | [INFO] [stdout] = note: the item `String` is already defined here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `Rng` is imported redundantly [INFO] [stdout] --> src/utils/mutate.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 8 | use rand::prelude::*; [INFO] [stdout] | ---------------- the item `Rng` is already imported here [INFO] [stdout] 9 | use rand::Rng; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `serde_json` is imported redundantly [INFO] [stdout] --> src/utils/read_models.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use serde_json; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] ::: src/main.rs:10:1 [INFO] [stdout] | [INFO] [stdout] 10 | extern crate serde_json; [INFO] [stdout] | ------------------------ the item `serde_json` is already imported here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `io` is imported redundantly [INFO] [stdout] --> src/utils/fasta_tools.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::io; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 5 | use std::io::Write; [INFO] [stdout] 6 | use std::*; [INFO] [stdout] | ------ the item `io` is already imported here [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `NeatRng` is imported redundantly [INFO] [stdout] --> src/utils/make_reads.rs:157:9 [INFO] [stdout] | [INFO] [stdout] 155 | use super::*; [INFO] [stdout] | -------- the item `NeatRng` is already imported here [INFO] [stdout] 156 | use rand::SeedableRng; [INFO] [stdout] 157 | use utils::neat_rng::NeatRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `Rng` is imported redundantly [INFO] [stdout] --> src/utils/mutate.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 8 | use rand::prelude::*; [INFO] [stdout] | ---------------- the item `Rng` is already imported here [INFO] [stdout] 9 | use rand::Rng; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `SeedableRng` is imported redundantly [INFO] [stdout] --> src/utils/mutate.rs:146:9 [INFO] [stdout] | [INFO] [stdout] 146 | use rand::SeedableRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] 147 | use utils::neat_rng::NeatRng; [INFO] [stdout] 148 | use super::*; [INFO] [stdout] | -------- the item `SeedableRng` is already imported here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `NeatRng` is imported redundantly [INFO] [stdout] --> src/utils/mutate.rs:147:9 [INFO] [stdout] | [INFO] [stdout] 147 | use utils::neat_rng::NeatRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 148 | use super::*; [INFO] [stdout] | -------- the item `NeatRng` is already imported here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `NeatRng` is imported redundantly [INFO] [stdout] --> src/utils/vcf_tools.rs:111:9 [INFO] [stdout] | [INFO] [stdout] 109 | use super::*; [INFO] [stdout] | -------- the item `NeatRng` is already imported here [INFO] [stdout] 110 | use std::path::Path; [INFO] [stdout] 111 | use utils::neat_rng::NeatRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `RngCore` is imported redundantly [INFO] [stdout] --> src/utils/neat_rng.rs:82:16 [INFO] [stdout] | [INFO] [stdout] 81 | use super::*; [INFO] [stdout] | -------- the item `RngCore` is already imported here [INFO] [stdout] 82 | use rand::{RngCore, SeedableRng}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `SeedableRng` is imported redundantly [INFO] [stdout] --> src/utils/neat_rng.rs:82:25 [INFO] [stdout] | [INFO] [stdout] 81 | use super::*; [INFO] [stdout] | -------- the item `SeedableRng` is already imported here [INFO] [stdout] 82 | use rand::{RngCore, SeedableRng}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `serde_json` is imported redundantly [INFO] [stdout] --> src/utils/read_models.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use serde_json; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] ::: src/main.rs:10:1 [INFO] [stdout] | [INFO] [stdout] 10 | extern crate serde_json; [INFO] [stdout] | ------------------------ the item `serde_json` is already imported here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `mutation_rate` and `produce_bam` are never read [INFO] [stdout] --> src/utils/config.rs:43:9 [INFO] [stdout] | [INFO] [stdout] 16 | pub struct RunConfiguration { [INFO] [stdout] | ---------------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 43 | pub mutation_rate: f64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 51 | 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:69:12 [INFO] [stdout] | [INFO] [stdout] 67 | impl QualityScoreModel { [INFO] [stdout] | ---------------------- associated items in this implementation [INFO] [stdout] 68 | // methods for QualityScoreModel objects [INFO] [stdout] 69 | pub fn new() -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 101 | pub fn display(&self) -> String { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 115 | pub fn display_it_all(&self) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 212 | 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] [stdout] warning: 8 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 9 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 45.76s [INFO] running `Command { std: "docker" "inspect" "f98ad12f3ffe22716b3f4f4bc3a1841c596aaeafc81b77b300975119ff1a7005", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f98ad12f3ffe22716b3f4f4bc3a1841c596aaeafc81b77b300975119ff1a7005", kill_on_drop: false }` [INFO] [stdout] f98ad12f3ffe22716b3f4f4bc3a1841c596aaeafc81b77b300975119ff1a7005