[INFO] cloning repository https://github.com/heathsc/lbtools
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/heathsc/lbtools" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fheathsc%2Flbtools", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fheathsc%2Flbtools'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 78c2784d307c79c80ea12564b8d099a460d00c4c
[INFO] checking heathsc/lbtools against try#86f78589b09557f70c9db3f56ad1921e0a9f76ef for pr-138438
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fheathsc%2Flbtools" "/workspace/builds/worker-0-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/heathsc/lbtools on toolchain 86f78589b09557f70c9db3f56ad1921e0a9f76ef
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+86f78589b09557f70c9db3f56ad1921e0a9f76ef" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/heathsc/lbtools
[INFO] finished tweaking git repo https://github.com/heathsc/lbtools
[INFO] tweaked toml for git repo https://github.com/heathsc/lbtools written to /workspace/builds/worker-0-tc2/source/Cargo.toml
[INFO] crate git repo https://github.com/heathsc/lbtools 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" "+86f78589b09557f70c9db3f56ad1921e0a9f76ef" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Blocking waiting for file lock on package cache
[ERROR] error running command: no output for 300 seconds
[INFO] checking heathsc/lbtools against try#86f78589b09557f70c9db3f56ad1921e0a9f76ef for pr-138438
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fheathsc%2Flbtools" "/workspace/builds/worker-0-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/heathsc/lbtools on toolchain 86f78589b09557f70c9db3f56ad1921e0a9f76ef
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+86f78589b09557f70c9db3f56ad1921e0a9f76ef" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/heathsc/lbtools
[INFO] finished tweaking git repo https://github.com/heathsc/lbtools
[INFO] tweaked toml for git repo https://github.com/heathsc/lbtools written to /workspace/builds/worker-0-tc2/source/Cargo.toml
[INFO] crate git repo https://github.com/heathsc/lbtools 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" "+86f78589b09557f70c9db3f56ad1921e0a9f76ef" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Blocking waiting for file lock on package cache
[ERROR] error running command: no output for 300 seconds
[INFO] checking heathsc/lbtools against try#86f78589b09557f70c9db3f56ad1921e0a9f76ef for pr-138438
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fheathsc%2Flbtools" "/workspace/builds/worker-0-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/heathsc/lbtools on toolchain 86f78589b09557f70c9db3f56ad1921e0a9f76ef
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+86f78589b09557f70c9db3f56ad1921e0a9f76ef" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/heathsc/lbtools
[INFO] finished tweaking git repo https://github.com/heathsc/lbtools
[INFO] tweaked toml for git repo https://github.com/heathsc/lbtools written to /workspace/builds/worker-0-tc2/source/Cargo.toml
[INFO] crate git repo https://github.com/heathsc/lbtools 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" "+86f78589b09557f70c9db3f56ad1921e0a9f76ef" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded special v0.9.0
[INFO] [stderr]   Downloaded compress_io v0.5.0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:1680c8fbd8dfb46fcd6d22e546df16ab0e007457dc29fcd9e987cdd5077fd1af" "/opt/rustwide/cargo-home/bin/cargo" "+86f78589b09557f70c9db3f56ad1921e0a9f76ef" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 6298c754678d7bb5c2c2adf15a0423f598ca8731e3bb92c75e3736f3abf3ce3a
[INFO] running `Command { std: "docker" "start" "-a" "6298c754678d7bb5c2c2adf15a0423f598ca8731e3bb92c75e3736f3abf3ce3a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "6298c754678d7bb5c2c2adf15a0423f598ca8731e3bb92c75e3736f3abf3ce3a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "6298c754678d7bb5c2c2adf15a0423f598ca8731e3bb92c75e3736f3abf3ce3a", kill_on_drop: false }`
[INFO] [stdout] 6298c754678d7bb5c2c2adf15a0423f598ca8731e3bb92c75e3736f3abf3ce3a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:1680c8fbd8dfb46fcd6d22e546df16ab0e007457dc29fcd9e987cdd5077fd1af" "/opt/rustwide/cargo-home/bin/cargo" "+86f78589b09557f70c9db3f56ad1921e0a9f76ef" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 4b8aa82dedd0298849f3e8757f95b8f29d8957fa7500be2ab6386f9d7113a5a1
[INFO] running `Command { std: "docker" "start" "-a" "4b8aa82dedd0298849f3e8757f95b8f29d8957fa7500be2ab6386f9d7113a5a1", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.153
[INFO] [stderr]    Compiling autocfg v1.1.0
[INFO] [stderr]     Checking utf8parse v0.2.1
[INFO] [stderr]     Checking cfg-if v1.0.0
[INFO] [stderr]    Compiling libm v0.2.8
[INFO] [stderr]    Compiling anyhow v1.0.79
[INFO] [stderr]     Checking colorchoice v1.0.0
[INFO] [stderr]     Checking anstyle v1.0.6
[INFO] [stderr]     Checking anstyle-query v1.0.2
[INFO] [stderr]     Checking iana-time-zone v0.1.60
[INFO] [stderr]    Compiling rustix v0.38.31
[INFO] [stderr]     Checking strsim v0.11.0
[INFO] [stderr]     Checking clap_lex v0.7.0
[INFO] [stderr]     Checking once_cell v1.19.0
[INFO] [stderr]     Checking log v0.4.20
[INFO] [stderr]     Checking memchr v2.7.1
[INFO] [stderr]    Compiling crossbeam-utils v0.8.19
[INFO] [stderr]     Checking linux-raw-sys v0.4.13
[INFO] [stderr]    Compiling proc-macro2 v1.0.78
[INFO] [stderr]     Checking anstyle-parse v0.2.3
[INFO] [stderr]     Checking termcolor v1.1.3
[INFO] [stderr]     Checking bitflags v2.4.2
[INFO] [stderr]    Compiling unicode-ident v1.0.12
[INFO] [stderr]     Checking lazy_static v1.4.0
[INFO] [stderr]     Checking thread_local v1.1.7
[INFO] [stderr]     Checking regex-syntax v0.6.29
[INFO] [stderr]     Checking fastrand v2.0.1
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]     Checking anstream v0.6.11
[INFO] [stderr]    Compiling num-traits v0.2.18
[INFO] [stderr]     Checking clap_builder v4.5.0
[INFO] [stderr]     Checking crossbeam-channel v0.5.11
[INFO] [stderr]     Checking aho-corasick v0.7.20
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]     Checking os_pipe v1.1.5
[INFO] [stderr]     Checking num_cpus v1.16.0
[INFO] [stderr]     Checking special v0.9.0
[INFO] [stderr]    Compiling quote v1.0.35
[INFO] [stderr]     Checking chrono v0.4.34
[INFO] [stderr]     Checking regex v1.7.3
[INFO] [stderr]     Checking clap v4.5.0
[INFO] [stderr]     Checking stderrlog v0.5.4
[INFO] [stderr]     Checking utils v0.3.1 (/opt/rustwide/workdir/utils)
[INFO] [stderr]     Checking tempfile v3.10.0
[INFO] [stderr]     Checking compress_io v0.5.0
[INFO] [stderr]     Checking lb_region_test v0.3.1 (/opt/rustwide/workdir/lb_region_test)
[INFO] [stderr]     Checking lb_norm v0.3.1 (/opt/rustwide/workdir/lb_norm)
[INFO] [stdout] warning: unused import: `path::Path`
[INFO] [stdout]  --> lb_region_test/src/process.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 |     path::Path,
[INFO] [stdout]   |     ^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around assigned value
[INFO] [stdout]    --> lb_region_test/src/process.rs:159:24
[INFO] [stdout]     |
[INFO] [stdout] 159 |             let mean = ((q1 + q2 + q3) / 3.0);
[INFO] [stdout]     |                        ^                    ^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_parens)]` on by default
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]     |
[INFO] [stdout] 159 -             let mean = ((q1 + q2 + q3) / 3.0);
[INFO] [stdout] 159 +             let mean = (q1 + q2 + q3) / 3.0;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `sync::Arc`
[INFO] [stdout]  --> lb_region_test/src/sample.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 |     sync::Arc,
[INFO] [stdout]   |     ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `path::Path`
[INFO] [stdout]  --> lb_region_test/src/process.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 |     path::Path,
[INFO] [stdout]   |     ^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around assigned value
[INFO] [stdout]    --> lb_region_test/src/process.rs:159:24
[INFO] [stdout]     |
[INFO] [stdout] 159 |             let mean = ((q1 + q2 + q3) / 3.0);
[INFO] [stdout]     |                        ^                    ^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_parens)]` on by default
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]     |
[INFO] [stdout] 159 -             let mean = ((q1 + q2 + q3) / 3.0);
[INFO] [stdout] 159 +             let mean = (q1 + q2 + q3) / 3.0;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `sync::Arc`
[INFO] [stdout]  --> lb_region_test/src/sample.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 |     sync::Arc,
[INFO] [stdout]   |     ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `ctg_list` is never read
[INFO] [stdout]   --> lb_region_test/src/config.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 8  | pub struct Config {
[INFO] [stdout]    |            ------ field in this struct
[INFO] [stdout] 9  |     sample_list: Vec<Sample>,
[INFO] [stdout] 10 |     ctg_list: Vec<Contig>,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `ctg_list` is never used
[INFO] [stdout]   --> lb_region_test/src/config.rs:30:12
[INFO] [stdout]    |
[INFO] [stdout] 15 | impl Config {
[INFO] [stdout]    | ----------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 30 |     pub fn ctg_list(&self) -> &[Contig] {
[INFO] [stdout]    |            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `ctg_list` is never read
[INFO] [stdout]   --> lb_region_test/src/config.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 8  | pub struct Config {
[INFO] [stdout]    |            ------ field in this struct
[INFO] [stdout] 9  |     sample_list: Vec<Sample>,
[INFO] [stdout] 10 |     ctg_list: Vec<Contig>,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `ctg_list` is never used
[INFO] [stdout]   --> lb_region_test/src/config.rs:30:12
[INFO] [stdout]    |
[INFO] [stdout] 15 | impl Config {
[INFO] [stdout]    | ----------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 30 |     pub fn ctg_list(&self) -> &[Contig] {
[INFO] [stdout]    |            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]    Compiling c2rust-bitfields-derive v0.2.1
[INFO] [stderr]     Checking c2rust-bitfields v0.3.0
[INFO] [stderr]     Checking r_htslib v0.14.0 (https://github.com/heathsc/r_htslib.git#9f8544ef)
[INFO] [stderr]     Checking lb_predict_cn v0.3.1 (/opt/rustwide/workdir/lb_predict_cn)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 7.54s
[INFO] running `Command { std: "docker" "inspect" "4b8aa82dedd0298849f3e8757f95b8f29d8957fa7500be2ab6386f9d7113a5a1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "4b8aa82dedd0298849f3e8757f95b8f29d8957fa7500be2ab6386f9d7113a5a1", kill_on_drop: false }`
[INFO] [stdout] 4b8aa82dedd0298849f3e8757f95b8f29d8957fa7500be2ab6386f9d7113a5a1