[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] 1704c33296911e5acc78832766651da2514582ad
[INFO] checking stela2502/bam_aligner against master#9f48dedc9763334a587c66558974635807a113ed for pr-137394
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fbam_aligner" "/workspace/builds/worker-2-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/stela2502/bam_aligner on toolchain 9f48dedc9763334a587c66558974635807a113ed
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+9f48dedc9763334a587c66558974635807a113ed" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[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-2-tc1/source/Cargo.toml
[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" "+9f48dedc9763334a587c66558974635807a113ed" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded rust-htslib v0.43.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:3959728d45483eb673ba100a951a6b9f5012970368db2a9e08e0ac9b67c8a5ad" "/opt/rustwide/cargo-home/bin/cargo" "+9f48dedc9763334a587c66558974635807a113ed" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] f8d9d13b0bc43a2c61eed6f0f9eea9910468e6b687fa080bfb3d9718d37bd0d0
[INFO] running `Command { std: "docker" "start" "-a" "f8d9d13b0bc43a2c61eed6f0f9eea9910468e6b687fa080bfb3d9718d37bd0d0", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "f8d9d13b0bc43a2c61eed6f0f9eea9910468e6b687fa080bfb3d9718d37bd0d0", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f8d9d13b0bc43a2c61eed6f0f9eea9910468e6b687fa080bfb3d9718d37bd0d0", kill_on_drop: false }`
[INFO] [stdout] f8d9d13b0bc43a2c61eed6f0f9eea9910468e6b687fa080bfb3d9718d37bd0d0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:3959728d45483eb673ba100a951a6b9f5012970368db2a9e08e0ac9b67c8a5ad" "/opt/rustwide/cargo-home/bin/cargo" "+9f48dedc9763334a587c66558974635807a113ed" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 06252bee484958057d1b0a650696dca85fe7b3143530c3e59ecd673b90e20576
[INFO] running `Command { std: "docker" "start" "-a" "06252bee484958057d1b0a650696dca85fe7b3143530c3e59ecd673b90e20576", kill_on_drop: false }`
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[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: 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: 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: 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:72:13
[INFO] [stdout]    |
[INFO] [stdout] 72 |         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:73:13
[INFO] [stdout]    |
[INFO] [stdout] 73 |         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:74:13
[INFO] [stdout]    |
[INFO] [stdout] 74 |         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:72:13
[INFO] [stdout]    |
[INFO] [stdout] 72 |         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:73:13
[INFO] [stdout]    |
[INFO] [stdout] 73 |         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:74:13
[INFO] [stdout]    |
[INFO] [stdout] 74 |         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 5m 13s
[INFO] running `Command { std: "docker" "inspect" "06252bee484958057d1b0a650696dca85fe7b3143530c3e59ecd673b90e20576", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "06252bee484958057d1b0a650696dca85fe7b3143530c3e59ecd673b90e20576", kill_on_drop: false }`
[INFO] [stdout] 06252bee484958057d1b0a650696dca85fe7b3143530c3e59ecd673b90e20576