[INFO] cloning repository https://github.com/stela2502/bam_aligner
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/stela2502/bam_aligner" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fbam_aligner", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fbam_aligner'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] c3e791f98da8af3f94b34fdef4adc18a49368067
[INFO] checking stela2502/bam_aligner against try#a2a6e871b05c7b8ecc9a3c8a20db1f39e995e399 for pr-145770
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fbam_aligner" "/workspace/builds/worker-5-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/stela2502/bam_aligner
[INFO] finished tweaking git repo https://github.com/stela2502/bam_aligner
[INFO] tweaked toml for git repo https://github.com/stela2502/bam_aligner written to /workspace/builds/worker-5-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/stela2502/bam_aligner on toolchain a2a6e871b05c7b8ecc9a3c8a20db1f39e995e399
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+a2a6e871b05c7b8ecc9a3c8a20db1f39e995e399" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/stela2502/bam_aligner 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" "+a2a6e871b05c7b8ecc9a3c8a20db1f39e995e399" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+a2a6e871b05c7b8ecc9a3c8a20db1f39e995e399" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] ba6d5cda109480ed678b53a58445f5060ba565abc9638fd9b0057f9cfd008bc4
[INFO] running `Command { std: "docker" "start" "-a" "ba6d5cda109480ed678b53a58445f5060ba565abc9638fd9b0057f9cfd008bc4", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "ba6d5cda109480ed678b53a58445f5060ba565abc9638fd9b0057f9cfd008bc4", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ba6d5cda109480ed678b53a58445f5060ba565abc9638fd9b0057f9cfd008bc4", kill_on_drop: false }`
[INFO] [stdout] ba6d5cda109480ed678b53a58445f5060ba565abc9638fd9b0057f9cfd008bc4
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+a2a6e871b05c7b8ecc9a3c8a20db1f39e995e399" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 43041bb722f69a82b435863dfbfb802426d7367634404b34412d4444f0b61089
[INFO] running `Command { std: "docker" "start" "-a" "43041bb722f69a82b435863dfbfb802426d7367634404b34412d4444f0b61089", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.158
[INFO] [stderr]    Compiling shlex v1.3.0
[INFO] [stderr]    Compiling pkg-config v0.3.30
[INFO] [stderr]    Compiling proc-macro2 v1.0.86
[INFO] [stderr]    Compiling unicode-ident v1.0.12
[INFO] [stderr]    Compiling vcpkg v0.2.15
[INFO] [stderr]    Compiling crossbeam-utils v0.8.20
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]     Checking memchr v2.7.4
[INFO] [stderr]    Compiling heck v0.5.0
[INFO] [stderr]     Checking tinyvec_macros v0.1.1
[INFO] [stderr]    Compiling rustversion v1.0.17
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling thiserror v1.0.63
[INFO] [stderr]    Compiling glob v0.3.1
[INFO] [stderr]     Checking tinyvec v1.8.0
[INFO] [stderr]    Compiling fs-utils v1.1.4
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[INFO] [stderr]     Checking anstyle-query v1.1.1
[INFO] [stderr]     Checking percent-encoding v2.3.1
[INFO] [stderr]     Checking is_terminal_polyfill v1.70.1
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[INFO] [stderr]     Checking anstyle v1.0.8
[INFO] [stderr]     Checking colorchoice v1.0.2
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[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking aho-corasick v1.1.3
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[INFO] [stderr]    Compiling cc v1.1.13
[INFO] [stderr]     Checking rayon v1.10.0
[INFO] [stderr]     Checking url v2.5.2
[INFO] [stderr]    Compiling openssl-src v300.3.1+3.3.1
[INFO] [stderr]    Compiling cmake v0.1.51
[INFO] [stderr]    Compiling openssl-sys v0.9.103
[INFO] [stderr]    Compiling libz-sys v1.1.19
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling curl-sys v0.4.74+curl-8.9.0
[INFO] [stderr]    Compiling hts-sys v2.1.4
[INFO] [stderr]     Checking regex-automata v0.4.7
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]     Checking regex v1.10.6
[INFO] [stderr]    Compiling thiserror-impl v1.0.63
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling clap_derive v4.5.13
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking clap v4.5.16
[INFO] [stderr]     Checking rust-htslib v0.43.1
[INFO] [stderr]     Checking bam_aligner v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `std::thread`
[INFO] [stdout]  --> src/bam_subset.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::thread;
[INFO] [stdout]   |     ^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::thread`
[INFO] [stdout]  --> src/bam_subset.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::thread;
[INFO] [stdout]   |     ^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `current_contig_start` is assigned to, but never used
[INFO] [stdout]   --> src/bam_subset.rs:60:33
[INFO] [stdout]    |
[INFO] [stdout] 60 |                         let mut current_contig_start = 0;
[INFO] [stdout]    |                                 ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_current_contig_start` instead
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `current_contig_start` is assigned to, but never used
[INFO] [stdout]   --> src/bam_subset.rs:60:33
[INFO] [stdout]    |
[INFO] [stdout] 60 |                         let mut current_contig_start = 0;
[INFO] [stdout]    |                                 ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_current_contig_start` instead
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `current_contig_start` is never read
[INFO] [stdout]   --> src/bam_subset.rs:82:33
[INFO] [stdout]    |
[INFO] [stdout] 82 | ...                   current_contig_start = start_pos;
[INFO] [stdout]    |                       ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout]    = note: `#[warn(unused_assignments)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `current_contig_start` is never read
[INFO] [stdout]   --> src/bam_subset.rs:82:33
[INFO] [stdout]    |
[INFO] [stdout] 82 | ...                   current_contig_start = start_pos;
[INFO] [stdout]    |                       ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout]    = note: `#[warn(unused_assignments)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Header` and `Record`
[INFO] [stdout]  --> src/main.rs:2:38
[INFO] [stdout]   |
[INFO] [stdout] 2 | use rust_htslib::bam::{Read, Reader, Record, Header};
[INFO] [stdout]   |                                      ^^^^^^  ^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Header` and `Record`
[INFO] [stdout]  --> src/main.rs:2:38
[INFO] [stdout]   |
[INFO] [stdout] 2 | use rust_htslib::bam::{Read, Reader, Record, Header};
[INFO] [stdout]   |                                      ^^^^^^  ^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `tid`
[INFO] [stdout]   --> src/main.rs:73:13
[INFO] [stdout]    |
[INFO] [stdout] 73 |         let tid = record.tid();
[INFO] [stdout]    |             ^^^ help: if this is intentional, prefix it with an underscore: `_tid`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `this_start`
[INFO] [stdout]   --> src/main.rs:74:13
[INFO] [stdout]    |
[INFO] [stdout] 74 |         let this_start = record.pos() as u32;
[INFO] [stdout]    |             ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_this_start`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `this_end`
[INFO] [stdout]   --> src/main.rs:75:13
[INFO] [stdout]    |
[INFO] [stdout] 75 |         let this_end = record.cigar().end_pos() as u32;
[INFO] [stdout]    |             ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_this_end`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `tid`
[INFO] [stdout]   --> src/main.rs:73:13
[INFO] [stdout]    |
[INFO] [stdout] 73 |         let tid = record.tid();
[INFO] [stdout]    |             ^^^ help: if this is intentional, prefix it with an underscore: `_tid`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `this_start`
[INFO] [stdout]   --> src/main.rs:74:13
[INFO] [stdout]    |
[INFO] [stdout] 74 |         let this_start = record.pos() as u32;
[INFO] [stdout]    |             ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_this_start`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `this_end`
[INFO] [stdout]   --> src/main.rs:75:13
[INFO] [stdout]    |
[INFO] [stdout] 75 |         let this_end = record.cigar().end_pos() as u32;
[INFO] [stdout]    |             ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_this_end`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 04s
[INFO] running `Command { std: "docker" "inspect" "43041bb722f69a82b435863dfbfb802426d7367634404b34412d4444f0b61089", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "43041bb722f69a82b435863dfbfb802426d7367634404b34412d4444f0b61089", kill_on_drop: false }`
[INFO] [stdout] 43041bb722f69a82b435863dfbfb802426d7367634404b34412d4444f0b61089
