[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 }`
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[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 4cb1394d7cb2ae73a2ba6b639a6cac12ede4ac34
[INFO] building xiexm1/kmertk against try#d79d87d4c0f7f0d0785ad6e493cf8cf718ed89a6 for pr-146237-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fxiexm1%2Fkmertk" "/workspace/builds/worker-7-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc2/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-7-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/xiexm1/kmertk on toolchain d79d87d4c0f7f0d0785ad6e493cf8cf718ed89a6
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+d79d87d4c0f7f0d0785ad6e493cf8cf718ed89a6" "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" "+d79d87d4c0f7f0d0785ad6e493cf8cf718ed89a6" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "rm" "-f" "7c577d60c6f0864ddf2aa313ff57e8ef3dc768c9c2682bfd5fd63782a8284fc7", kill_on_drop: false }`
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[INFO] [stdout] f70a5d60df45d810e424c54429a3b197c7d6cc6e2134025e30b88d7cbb22a824
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[INFO] [stderr]    Compiling matrixmultiply v0.3.9
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[INFO] [stderr]    Compiling clap_derive v4.5.32
[INFO] [stderr]    Compiling indicatif v0.17.11
[INFO] [stderr]    Compiling flate2 v1.1.1
[INFO] [stderr]    Compiling bio-types v1.0.4
[INFO] [stderr]    Compiling nalgebra v0.29.0
[INFO] [stderr]    Compiling serde v1.0.219
[INFO] [stderr]    Compiling clap v4.5.36
[INFO] [stderr]    Compiling vec_map v0.8.2
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[INFO] [stderr]    Compiling csv v1.3.1
[INFO] [stderr]    Compiling multimap v0.9.1
[INFO] [stderr]    Compiling statrs v0.16.1
[INFO] [stderr]    Compiling bio v1.6.0
[INFO] [stderr]    Compiling 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)]` (part of `#[warn(unused)]`) 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)]` (part of `#[warn(unused)]`) 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<P: AsRef<Path>>(file_path: P) -> io::Result<usize> {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) 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<usize>,        // 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 1m 44s
[INFO] running `Command { std: "docker" "inspect" "f70a5d60df45d810e424c54429a3b197c7d6cc6e2134025e30b88d7cbb22a824", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f70a5d60df45d810e424c54429a3b197c7d6cc6e2134025e30b88d7cbb22a824", kill_on_drop: false }`
[INFO] [stdout] f70a5d60df45d810e424c54429a3b197c7d6cc6e2134025e30b88d7cbb22a824
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+d79d87d4c0f7f0d0785ad6e493cf8cf718ed89a6" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 49ec4c144fb69f9c809e500994d2dbda39f54b6afe1f23e1b0879b3ca3b2e755
[INFO] running `Command { std: "docker" "start" "-a" "49ec4c144fb69f9c809e500994d2dbda39f54b6afe1f23e1b0879b3ca3b2e755", kill_on_drop: false }`
[INFO] [stderr]    Compiling 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)]` (part of `#[warn(unused)]`) 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)]` (part of `#[warn(unused)]`) 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<P: AsRef<Path>>(file_path: P) -> io::Result<usize> {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) 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<usize>,        // 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 `test` profile [unoptimized + debuginfo] target(s) in 0.89s
[INFO] running `Command { std: "docker" "inspect" "49ec4c144fb69f9c809e500994d2dbda39f54b6afe1f23e1b0879b3ca3b2e755", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "49ec4c144fb69f9c809e500994d2dbda39f54b6afe1f23e1b0879b3ca3b2e755", kill_on_drop: false }`
[INFO] [stdout] 49ec4c144fb69f9c809e500994d2dbda39f54b6afe1f23e1b0879b3ca3b2e755