[INFO] cloning repository https://github.com/xiexm1/kmertk [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/xiexm1/kmertk" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fxiexm1%2Fkmertk", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fxiexm1%2Fkmertk'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 4cb1394d7cb2ae73a2ba6b639a6cac12ede4ac34 [INFO] checking xiexm1/kmertk against master#ba412a6e70ac84641be7764d088acabd0eb3fa39 for pr-145457 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fxiexm1%2Fkmertk" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/xiexm1/kmertk [INFO] finished tweaking git repo https://github.com/xiexm1/kmertk [INFO] tweaked toml for git repo https://github.com/xiexm1/kmertk written to /workspace/builds/worker-0-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/xiexm1/kmertk on toolchain ba412a6e70ac84641be7764d088acabd0eb3fa39 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ba412a6e70ac84641be7764d088acabd0eb3fa39" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/xiexm1/kmertk 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" "+ba412a6e70ac84641be7764d088acabd0eb3fa39" "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-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+ba412a6e70ac84641be7764d088acabd0eb3fa39" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] cc1b1409f973a11215288ac75d9f15d4aa9e6f372abf5a63ade45af2d1611e27 [INFO] running `Command { std: "docker" "start" "-a" "cc1b1409f973a11215288ac75d9f15d4aa9e6f372abf5a63ade45af2d1611e27", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "cc1b1409f973a11215288ac75d9f15d4aa9e6f372abf5a63ade45af2d1611e27", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "cc1b1409f973a11215288ac75d9f15d4aa9e6f372abf5a63ade45af2d1611e27", kill_on_drop: false }` [INFO] [stdout] cc1b1409f973a11215288ac75d9f15d4aa9e6f372abf5a63ade45af2d1611e27 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+ba412a6e70ac84641be7764d088acabd0eb3fa39" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 8ca7273d1e73ed1b3ac7ebc2c056ccbb86c566b78aaae450bea23b89b08e8182 [INFO] running `Command { std: "docker" "start" "-a" "8ca7273d1e73ed1b3ac7ebc2c056ccbb86c566b78aaae450bea23b89b08e8182", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.94 [INFO] [stderr] Compiling unicode-ident v1.0.18 [INFO] [stderr] 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v0.2.19 [INFO] [stderr] Compiling matrixmultiply v0.3.9 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Checking wide v0.7.32 [INFO] [stderr] Compiling quote v1.0.40 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking crossbeam-epoch v0.9.18 [INFO] [stderr] Checking lazy_static v1.5.0 [INFO] [stderr] Checking aho-corasick v1.1.3 [INFO] [stderr] Checking colorchoice v1.0.3 [INFO] [stderr] Compiling rayon-core v1.12.1 [INFO] [stderr] Checking is_terminal_polyfill v1.70.1 [INFO] [stderr] Checking anstyle v1.0.10 [INFO] [stderr] Checking anstyle-query v1.1.2 [INFO] [stderr] Compiling syn v2.0.100 [INFO] [stderr] Checking hashbrown v0.15.2 [INFO] [stderr] Compiling portable-atomic v1.11.0 [INFO] [stderr] Compiling anyhow v1.0.98 [INFO] [stderr] Checking either v1.15.0 [INFO] [stderr] Checking equivalent v1.0.2 [INFO] [stderr] Checking anstream v0.6.18 [INFO] [stderr] Checking csv-core v0.1.12 [INFO] [stderr] Checking crossbeam-deque v0.8.6 [INFO] [stderr] Checking 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thiserror-impl v1.0.69 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling clap_derive v4.5.32 [INFO] [stderr] Compiling strum_macros v0.25.3 [INFO] [stderr] Checking enum-map v2.7.3 [INFO] [stderr] Checking clap v4.5.36 [INFO] [stderr] Checking bio-types v1.0.4 [INFO] [stderr] Checking nalgebra v0.29.0 [INFO] [stderr] Checking multimap v0.9.1 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking csv v1.3.1 [INFO] [stderr] Checking statrs v0.16.1 [INFO] [stderr] Checking bio v1.6.0 [INFO] [stderr] Checking kmertk v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `rand::seq::SliceRandom` [INFO] [stdout] --> src/modules/distance.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | use rand::seq::SliceRandom; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::utils::read_kmers` [INFO] [stdout] --> src/modules/miniset.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use crate::utils::read_kmers; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `parse_fasta` [INFO] [stdout] --> src/modules/collection.rs:9:32 [INFO] [stdout] | [INFO] [stdout] 9 | use crate::utils::{read_kmers, parse_fasta, fasta_to_map}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::seq::SliceRandom` [INFO] [stdout] --> src/modules/distance.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | use rand::seq::SliceRandom; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::utils::read_kmers` [INFO] [stdout] --> src/modules/miniset.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use crate::utils::read_kmers; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `parse_fasta` [INFO] [stdout] --> src/modules/collection.rs:9:32 [INFO] [stdout] | [INFO] [stdout] 9 | use crate::utils::{read_kmers, parse_fasta, fasta_to_map}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `text` [INFO] [stdout] --> src/modules/collection.rs:157:22 [INFO] [stdout] | [INFO] [stdout] 157 | fn find_crispr_match(text: &[u8], pattern: &[u8]) -> bool { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_text` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `count_sequences` is never used [INFO] [stdout] --> src/utils/fasta.rs:55:8 [INFO] [stdout] | [INFO] [stdout] 55 | pub fn count_sequences>(file_path: P) -> io::Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `gene_hits` is never read [INFO] [stdout] --> src/modules/miniset.rs:41:5 [INFO] [stdout] | [INFO] [stdout] 37 | struct Data { [INFO] [stdout] | ---- field in this struct [INFO] [stdout] ... [INFO] [stdout] 41 | gene_hits: Vec, // 记录每个基因被多少k-mer覆盖 [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `flag`, `position`, `cigar`, and `sequence` are never read [INFO] [stdout] --> src/modules/collection.rs:81:5 [INFO] [stdout] | [INFO] [stdout] 79 | struct SamAlignment { [INFO] [stdout] | ------------ fields in this struct [INFO] [stdout] 80 | query_id: String, [INFO] [stdout] 81 | flag: u16, [INFO] [stdout] | ^^^^ [INFO] [stdout] 82 | ref_id: String, [INFO] [stdout] 83 | position: usize, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 84 | cigar: String, [INFO] [stdout] | ^^^^^ [INFO] [stdout] 85 | sequence: String, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `count_indels` is never used [INFO] [stdout] --> src/modules/collection.rs:91:8 [INFO] [stdout] | [INFO] [stdout] 89 | impl SamAlignment { [INFO] [stdout] | ----------------- method in this implementation [INFO] [stdout] 90 | // 计算插入删除数量 [INFO] [stdout] 91 | fn count_indels(&self) -> usize { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `strand`, `position`, `sequence`, and `mismatches` are never read [INFO] [stdout] --> src/modules/collection.rs:121:5 [INFO] [stdout] | [INFO] [stdout] 119 | struct BowtieAlignment { [INFO] [stdout] | --------------- fields in this struct [INFO] [stdout] 120 | query_id: String, [INFO] [stdout] 121 | strand: char, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] 122 | ref_id: String, [INFO] [stdout] 123 | position: usize, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 124 | sequence: String, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 125 | mismatches: Vec<(usize, char, char)>, // 位置，参考碱基，查询碱基 [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `text` [INFO] [stdout] --> src/modules/collection.rs:157:22 [INFO] [stdout] | [INFO] [stdout] 157 | fn find_crispr_match(text: &[u8], pattern: &[u8]) -> bool { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_text` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `count_sequences` is never used [INFO] [stdout] --> src/utils/fasta.rs:55:8 [INFO] [stdout] | [INFO] [stdout] 55 | pub fn count_sequences>(file_path: P) -> io::Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `gene_hits` is never read [INFO] [stdout] --> src/modules/miniset.rs:41:5 [INFO] [stdout] | [INFO] [stdout] 37 | struct Data { [INFO] [stdout] | ---- field in this struct [INFO] [stdout] ... [INFO] [stdout] 41 | gene_hits: Vec, // 记录每个基因被多少k-mer覆盖 [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `flag`, `position`, `cigar`, and `sequence` are never read [INFO] [stdout] --> src/modules/collection.rs:81:5 [INFO] [stdout] | [INFO] [stdout] 79 | struct SamAlignment { [INFO] [stdout] | ------------ fields in this struct [INFO] [stdout] 80 | query_id: String, [INFO] [stdout] 81 | flag: u16, [INFO] [stdout] | ^^^^ [INFO] [stdout] 82 | ref_id: String, [INFO] [stdout] 83 | position: usize, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 84 | cigar: String, [INFO] [stdout] | ^^^^^ [INFO] [stdout] 85 | sequence: String, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `count_indels` is never used [INFO] [stdout] --> src/modules/collection.rs:91:8 [INFO] [stdout] | [INFO] [stdout] 89 | impl SamAlignment { [INFO] [stdout] | ----------------- method in this implementation [INFO] [stdout] 90 | // 计算插入删除数量 [INFO] [stdout] 91 | fn count_indels(&self) -> usize { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `strand`, `position`, `sequence`, and `mismatches` are never read [INFO] [stdout] --> src/modules/collection.rs:121:5 [INFO] [stdout] | [INFO] [stdout] 119 | struct BowtieAlignment { [INFO] [stdout] | --------------- fields in this struct [INFO] [stdout] 120 | query_id: String, [INFO] [stdout] 121 | strand: char, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] 122 | ref_id: String, [INFO] [stdout] 123 | position: usize, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 124 | sequence: String, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 125 | mismatches: Vec<(usize, char, char)>, // 位置，参考碱基，查询碱基 [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 41.13s [INFO] running `Command { std: "docker" "inspect" "8ca7273d1e73ed1b3ac7ebc2c056ccbb86c566b78aaae450bea23b89b08e8182", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8ca7273d1e73ed1b3ac7ebc2c056ccbb86c566b78aaae450bea23b89b08e8182", kill_on_drop: false }` [INFO] [stdout] 8ca7273d1e73ed1b3ac7ebc2c056ccbb86c566b78aaae450bea23b89b08e8182