[INFO] cloning repository https://github.com/stela2502/bam_tide
[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_tide" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fbam_tide", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fbam_tide'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 141c3fbd5c93110de7bd54848c12676ab9eb67d8
[INFO] checking stela2502/bam_tide/141c3fbd5c93110de7bd54848c12676ab9eb67d8 against master#4455c8937007f3cc3c078375a335d86dbab391ce for pr-140956
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fbam_tide" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/stela2502/bam_tide
[INFO] finished tweaking git repo https://github.com/stela2502/bam_tide
[INFO] tweaked toml for git repo https://github.com/stela2502/bam_tide written to /workspace/builds/worker-5-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/stela2502/bam_tide on toolchain 4455c8937007f3cc3c078375a335d86dbab391ce
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+4455c8937007f3cc3c078375a335d86dbab391ce" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/stela2502/bam_tide 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" "+4455c8937007f3cc3c078375a335d86dbab391ce" "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
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded noodles-core v0.10.0
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+4455c8937007f3cc3c078375a335d86dbab391ce" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 99097527422a121d457492ea23ec5db332be6c93b93fa917eaf6127f1f3b16d5
[INFO] running `Command { std: "docker" "start" "-a" "99097527422a121d457492ea23ec5db332be6c93b93fa917eaf6127f1f3b16d5", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "99097527422a121d457492ea23ec5db332be6c93b93fa917eaf6127f1f3b16d5", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "99097527422a121d457492ea23ec5db332be6c93b93fa917eaf6127f1f3b16d5", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+4455c8937007f3cc3c078375a335d86dbab391ce" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "start" "-a" "cddd63b74f1a23aca302c5c51ab43c994564b6e1692ceb7467ba9ddb90b2e56f", kill_on_drop: false }`
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[INFO] [stderr]     Checking futures-executor v0.3.31
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[INFO] [stderr]     Checking bigtools v0.5.6
[INFO] [stderr]     Checking cargo_metadata v0.17.0
[INFO] [stderr]     Checking rustody v2.2.5 (https://github.com/stela2502/Rustody?branch=main2#c0f12052)
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[INFO] [stderr]     Checking bam_tide v0.4.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `std::thread::Builder`
[INFO] [stdout]  --> src/bed_data/bed_data.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use std::thread::Builder;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::thread::Builder`
[INFO] [stdout]  --> src/bed_data/bed_data.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use std::thread::Builder;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `flate2::read::GzDecoder`
[INFO] [stdout]    --> src/mutation_processor.rs:267:9
[INFO] [stdout]     |
[INFO] [stdout] 267 |     use flate2::read::GzDecoder;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs::File`
[INFO] [stdout]    --> src/mutation_processor.rs:268:9
[INFO] [stdout]     |
[INFO] [stdout] 268 |     use std::fs::File;
[INFO] [stdout]     |         ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `BufRead` and `BufReader`
[INFO] [stdout]    --> src/mutation_processor.rs:269:19
[INFO] [stdout]     |
[INFO] [stdout] 269 |     use std::io::{BufRead, BufReader};
[INFO] [stdout]     |                   ^^^^^^^  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused `Result` that must be used
[INFO] [stdout]    --> src/mutation_processor.rs:345:9
[INFO] [stdout]     |
[INFO] [stdout] 345 |         gex.write_sparse( file_path.clone(), &idx, 0 );
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stdout]     = note: `#[warn(unused_must_use)]` on by default
[INFO] [stdout] help: use `let _ = ...` to ignore the resulting value
[INFO] [stdout]     |
[INFO] [stdout] 345 |         let _ = gex.write_sparse( file_path.clone(), &idx, 0 );
[INFO] [stdout]     |         +++++++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs::File`
[INFO] [stdout]  --> tests/test_bowte2mtx.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::fs::File;
[INFO] [stdout]   |     ^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::BufReader`
[INFO] [stdout]  --> tests/test_bowte2mtx.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use std::io::BufReader;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::BufRead`
[INFO] [stdout]  --> tests/test_bowte2mtx.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::io::BufRead;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::HashMap`
[INFO] [stdout]  --> tests/test_bowte2mtx.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use std::collections::HashMap;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `super::*`
[INFO] [stdout]  --> tests/test_bed_data.rs:3:9
[INFO] [stdout]   |
[INFO] [stdout] 3 |     use super::*;
[INFO] [stdout]   |         ^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Value`
[INFO] [stdout]  --> tests/test_bed_data.rs:5:39
[INFO] [stdout]   |
[INFO] [stdout] 5 |     use bam_tide::bed_data::{BedData, Value}; // Adjust the path if needed
[INFO] [stdout]   |                                       ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `output_str`
[INFO] [stdout]   --> tests/test_bowte2mtx.rs:60:9
[INFO] [stdout]    |
[INFO] [stdout] 60 |     let output_str = String::from_utf8_lossy(&output.stdout);
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_str`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::HashMap`
[INFO] [stdout]  --> tests/integration_tests.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::collections::HashMap;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs::File`
[INFO] [stdout]  --> tests/test_bam2bedgraph.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::fs::File;
[INFO] [stdout]   |     ^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs`
[INFO] [stdout]  --> tests/test_bam2bedgraph.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::fs;
[INFO] [stdout]   |     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::BufReader`
[INFO] [stdout]  --> tests/test_bam2bedgraph.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use std::io::BufReader;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::BufRead`
[INFO] [stdout]  --> tests/test_bam2bedgraph.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::io::BufRead;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::HashMap`
[INFO] [stdout]  --> tests/test_bam2bedgraph.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use std::collections::HashMap;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0061]: this function takes 9 arguments but 8 arguments were supplied
[INFO] [stdout]    --> tests/integration_tests.rs:28:17
[INFO] [stdout]     |
[INFO] [stdout] 28  |     let data =  BedData::new( bam_file, 50, 1, &AnalysisType::Bulk, &b"CR", &b"No", false, false );
[INFO] [stdout]     |                 ^^^^^^^^^^^^---------------------------------------------------------------------- argument #9 of type `u8` is missing
[INFO] [stdout]     |
[INFO] [stdout] note: associated function defined here
[INFO] [stdout]    --> /opt/rustwide/workdir/src/bed_data/bed_data.rs:235:12
[INFO] [stdout]     |
[INFO] [stdout] 235 |     pub fn new(bam_file: &str , bin_width: usize, threads:usize, 
[INFO] [stdout]     |            ^^^
[INFO] [stdout] help: provide the argument
[INFO] [stdout]     |
[INFO] [stdout] 28  -     let data =  BedData::new( bam_file, 50, 1, &AnalysisType::Bulk, &b"CR", &b"No", false, false );
[INFO] [stdout] 28  +     let data =  BedData::new(bam_file, 50, 1, &AnalysisType::Bulk, &b"CR", &b"No", false, false, /* u8 */);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0061]: this function takes 9 arguments but 8 arguments were supplied
[INFO] [stdout]    --> tests/integration_tests.rs:57:17
[INFO] [stdout]     |
[INFO] [stdout] 57  |     let data =  BedData::new( bam_file, 50, 1, &AnalysisType::Bulk, &b"CR", &b"No", false, false );
[INFO] [stdout]     |                 ^^^^^^^^^^^^---------------------------------------------------------------------- argument #9 of type `u8` is missing
[INFO] [stdout]     |
[INFO] [stdout] note: associated function defined here
[INFO] [stdout]    --> /opt/rustwide/workdir/src/bed_data/bed_data.rs:235:12
[INFO] [stdout]     |
[INFO] [stdout] 235 |     pub fn new(bam_file: &str , bin_width: usize, threads:usize, 
[INFO] [stdout]     |            ^^^
[INFO] [stdout] help: provide the argument
[INFO] [stdout]     |
[INFO] [stdout] 57  -     let data =  BedData::new( bam_file, 50, 1, &AnalysisType::Bulk, &b"CR", &b"No", false, false );
[INFO] [stdout] 57  +     let data =  BedData::new(bam_file, 50, 1, &AnalysisType::Bulk, &b"CR", &b"No", false, false, /* u8 */);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `output_str`
[INFO] [stdout]   --> tests/test_bam2bedgraph.rs:55:9
[INFO] [stdout]    |
[INFO] [stdout] 55 |     let output_str = String::from_utf8_lossy(&output.stdout);
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_str`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0061`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `bam_tide` (test "integration_tests") due to 2 previous errors; 1 warning emitted
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] running `Command { std: "docker" "inspect" "cddd63b74f1a23aca302c5c51ab43c994564b6e1692ceb7467ba9ddb90b2e56f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "cddd63b74f1a23aca302c5c51ab43c994564b6e1692ceb7467ba9ddb90b2e56f", kill_on_drop: false }`
[INFO] [stdout] cddd63b74f1a23aca302c5c51ab43c994564b6e1692ceb7467ba9ddb90b2e56f