[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 try#2cbf9c3ff35600794d69a7dc7ab399810a067910 for pr-129249-2
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fxiexm1%2Fkmertk" "/workspace/builds/worker-0-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-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-0-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/xiexm1/kmertk on toolchain 2cbf9c3ff35600794d69a7dc7ab399810a067910
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+2cbf9c3ff35600794d69a7dc7ab399810a067910" "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" "+2cbf9c3ff35600794d69a7dc7ab399810a067910" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,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" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:3a6becf2bc8dde7f3fa57ede90e4f284e72d296796fc446bbb1e2c7cc0530151" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 42817723f60c20fdfee2703185452c4dadd90855e3b0b7d8d5d3eeb799f1313d
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[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "42817723f60c20fdfee2703185452c4dadd90855e3b0b7d8d5d3eeb799f1313d" "/opt/rustwide/cargo-home/bin/cargo" "+2cbf9c3ff35600794d69a7dc7ab399810a067910" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "42817723f60c20fdfee2703185452c4dadd90855e3b0b7d8d5d3eeb799f1313d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "42817723f60c20fdfee2703185452c4dadd90855e3b0b7d8d5d3eeb799f1313d" "/opt/rustwide/cargo-home/bin/cargo" "+2cbf9c3ff35600794d69a7dc7ab399810a067910" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling libm v0.2.11
[INFO] [stderr]    Compiling zerocopy v0.8.24
[INFO] [stderr]    Compiling serde v1.0.219
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling rustversion v1.0.20
[INFO] [stderr]     Checking bytemuck v1.22.0
[INFO] [stderr]    Compiling proc-macro2 v1.0.94
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[INFO] [stderr]     Checking aho-corasick v1.1.3
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[INFO] [stderr]    Compiling portable-atomic v1.11.0
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[INFO] [stderr]     Checking console v0.15.11
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[INFO] [stderr]     Checking miniz_oxide v0.8.8
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking rand_core v0.6.4
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[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling quote v1.0.40
[INFO] [stderr]     Checking itertools v0.11.0
[INFO] [stderr]     Checking strum v0.25.0
[INFO] [stderr]     Checking editdistancek v1.0.2
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[INFO] [stderr]     Checking rayon v1.10.0
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[INFO] [stderr]     Checking num-traits v0.2.19
[INFO] [stderr]     Checking wide v0.7.32
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[INFO] [stderr]     Checking regex v1.11.1
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[INFO] [stderr]    Compiling serde_derive v1.0.219
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[INFO] [stderr]    Compiling strum_macros v0.26.4
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[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)]` (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 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: 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] [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 39.71s
[INFO] running `Command { std: "docker" "inspect" "42817723f60c20fdfee2703185452c4dadd90855e3b0b7d8d5d3eeb799f1313d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "42817723f60c20fdfee2703185452c4dadd90855e3b0b7d8d5d3eeb799f1313d", kill_on_drop: false }`
[INFO] [stdout] 42817723f60c20fdfee2703185452c4dadd90855e3b0b7d8d5d3eeb799f1313d
