[INFO] cloning repository https://github.com/stela2502/quantify_bam
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/stela2502/quantify_bam" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fquantify_bam", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fquantify_bam'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] efd1f6ab5ebc7197ac7629c5acb13fc06aebb110
[INFO] documenting stela2502/quantify_bam against 1.86.0 for beta-1.87-rustdoc-2
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fquantify_bam" "/workspace/builds/worker-1-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-1-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/stela2502/quantify_bam on toolchain 1.86.0
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.86.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/stela2502/quantify_bam
[INFO] finished tweaking git repo https://github.com/stela2502/quantify_bam
[INFO] tweaked toml for git repo https://github.com/stela2502/quantify_bam written to /workspace/builds/worker-1-tc1/source/Cargo.toml
[INFO] crate git repo https://github.com/stela2502/quantify_bam 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" "+1.86.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Updating git repository `https://github.com/stela2502/Rustody`
[INFO] [stderr]     Updating git repository `https://github.com/COMBINE-lab/kmers`
[INFO] [stderr]     Blocking waiting for file lock on package cache
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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:b0b074c097205a61b89e8ad263052f976b2b332c4dc5f02aef1fe52501660d6e" "/opt/rustwide/cargo-home/bin/cargo" "+1.86.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 1f1c0b6d5d6cbb8356888db6360f8234901c6c7a296bab2469fafbbe5fab86c6
[INFO] running `Command { std: "docker" "start" "-a" "1f1c0b6d5d6cbb8356888db6360f8234901c6c7a296bab2469fafbbe5fab86c6", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "1f1c0b6d5d6cbb8356888db6360f8234901c6c7a296bab2469fafbbe5fab86c6", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "1f1c0b6d5d6cbb8356888db6360f8234901c6c7a296bab2469fafbbe5fab86c6", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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:b0b074c097205a61b89e8ad263052f976b2b332c4dc5f02aef1fe52501660d6e" "/opt/rustwide/cargo-home/bin/cargo" "+1.86.0" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] f8e836567809b1f8e28b516e7ca3c0068fd5267071384a51bdaaa1e3e2617d3e
[INFO] running `Command { std: "docker" "start" "-a" "f8e836567809b1f8e28b516e7ca3c0068fd5267071384a51bdaaa1e3e2617d3e", kill_on_drop: false }`
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[INFO] [stderr]  Documenting quantify_bam v0.4.3 (/opt/rustwide/workdir)
[INFO] [stderr]     Checking quantify_bam v0.4.3 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unexpected `cfg` condition value: `write`
[INFO] [stdout]  --> src/value.rs:4:12
[INFO] [stdout]   |
[INFO] [stdout] 4 | #[cfg_attr(feature = "write", derive(Serialize, Deserialize))]
[INFO] [stdout]   |            ^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]   |
[INFO] [stdout]   = note: no expected values for `feature`
[INFO] [stdout]   = help: consider adding `write` as a feature in `Cargo.toml`
[INFO] [stdout]   = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]   = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rustody::analysis::bam_flag::BamFlag`
[INFO] [stdout]   --> src/main_logics.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use rustody::analysis::bam_flag::BamFlag;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Cigar` and `Record`
[INFO] [stdout]   --> src/main_logics.rs:22:46
[INFO] [stdout]    |
[INFO] [stdout] 22 | use rust_htslib::bam::{Reader,Read, record::{Record, Cigar}};
[INFO] [stdout]    |                                              ^^^^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `write`
[INFO] [stdout]  --> src/value.rs:4:12
[INFO] [stdout]   |
[INFO] [stdout] 4 | #[cfg_attr(feature = "write", derive(Serialize, Deserialize))]
[INFO] [stdout]   |            ^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]   |
[INFO] [stdout]   = note: no expected values for `feature`
[INFO] [stdout]   = help: consider adding `write` as a feature in `Cargo.toml`
[INFO] [stdout]   = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]   = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/main_logics.rs:424:17
[INFO] [stdout]     |
[INFO] [stdout] 423 |                   todo!("Handle this case when I have more brainpower.");
[INFO] [stdout]     |                   ------------------------------------------------------ any code following this expression is unreachable
[INFO] [stdout] 424 | /                 let mate_gene_result = match match_type {
[INFO] [stdout] 425 | |                     MatchType::Overlap => gtf.match_cigar_to_gene_overlap(
[INFO] [stdout] 426 | |                         &mate.chromosome,
[INFO] [stdout] 427 | |                         &mate.cigar,
[INFO] [stdout] ...   |
[INFO] [stdout] 436 | |                     ),
[INFO] [stdout] 437 | |                 };
[INFO] [stdout]     | |__________________^ unreachable statement
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unreachable_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `header_view`
[INFO] [stdout]    --> src/main_logics.rs:140:9
[INFO] [stdout]     |
[INFO] [stdout] 140 |     let header_view = Header::from_template(reader.header() );
[INFO] [stdout]     |         ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_header_view`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/main_logics.rs:139:9
[INFO] [stdout]     |
[INFO] [stdout] 139 |     let mut reader = Reader::from_path( bam_file  ).unwrap();
[INFO] [stdout]     |         ----^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate`
[INFO] [stdout]    --> src/main_logics.rs:422:25
[INFO] [stdout]     |
[INFO] [stdout] 422 |             if let Some(mate) = mate_read {
[INFO] [stdout]     |                         ^^^^ help: if this is intentional, prefix it with an underscore: `_mate`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 49s
[INFO] [stderr]    Generated /opt/rustwide/target/doc/quantify_bam/index.html and 2 other files
[INFO] running `Command { std: "docker" "inspect" "f8e836567809b1f8e28b516e7ca3c0068fd5267071384a51bdaaa1e3e2617d3e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f8e836567809b1f8e28b516e7ca3c0068fd5267071384a51bdaaa1e3e2617d3e", kill_on_drop: false }`
[INFO] [stdout] f8e836567809b1f8e28b516e7ca3c0068fd5267071384a51bdaaa1e3e2617d3e
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-e" "DOCS_RS=1" "-e" "RUSTC_BOOTSTRAP=1" "-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:b0b074c097205a61b89e8ad263052f976b2b332c4dc5f02aef1fe52501660d6e" "/opt/rustwide/cargo-home/bin/cargo" "+1.86.0" "rustdoc" "--lib" "-Zrustdoc-map" "--config" "build.rustdocflags=[\"--cfg\", \"docsrs\", \"-Z\", \"unstable-options\", \"--document-private-items\"]" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] feb723d53b17a796f51ef7622924b6e74ff6bbc48140f0848aaebfaa1ff009a8
[INFO] running `Command { std: "docker" "start" "-a" "feb723d53b17a796f51ef7622924b6e74ff6bbc48140f0848aaebfaa1ff009a8", kill_on_drop: false }`
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[INFO] [stderr]    Compiling thiserror v1.0.69
[INFO] [stderr]    Compiling thiserror v2.0.11
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[INFO] [stderr]    Compiling syn v2.0.98
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[INFO] [stderr]    Compiling serde_derive v1.0.217
[INFO] [stderr]    Compiling icu_provider_macros v1.5.0
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[INFO] [stderr]     Checking icu_properties v1.5.1
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[INFO] [stderr]  Documenting quantify_bam v0.4.3 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unexpected `cfg` condition value: `write`
[INFO] [stdout]  --> src/value.rs:4:12
[INFO] [stdout]   |
[INFO] [stdout] 4 | #[cfg_attr(feature = "write", derive(Serialize, Deserialize))]
[INFO] [stdout]   |            ^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]   |
[INFO] [stdout]   = note: no expected values for `feature`
[INFO] [stdout]   = help: consider adding `write` as a feature in `Cargo.toml`
[INFO] [stdout]   = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]   = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 25.47s
[INFO] [stderr]    Generated /opt/rustwide/target/doc/quantify_bam/index.html
[INFO] running `Command { std: "docker" "inspect" "feb723d53b17a796f51ef7622924b6e74ff6bbc48140f0848aaebfaa1ff009a8", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "feb723d53b17a796f51ef7622924b6e74ff6bbc48140f0848aaebfaa1ff009a8", kill_on_drop: false }`
[INFO] [stdout] feb723d53b17a796f51ef7622924b6e74ff6bbc48140f0848aaebfaa1ff009a8
