[INFO] cloning repository https://github.com/lorewar2/bio_exp
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/lorewar2/bio_exp" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Florewar2%2Fbio_exp", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Florewar2%2Fbio_exp'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 854a34d5f320c34e62f6a23f222971eb9edacc10
[INFO] checking lorewar2/bio_exp against master#1f12b9b0fdbe735968ac002792a720f0ba4faca6 for crater-rollup-uwu
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Florewar2%2Fbio_exp" "/workspace/builds/worker-3-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/lorewar2/bio_exp on toolchain 1f12b9b0fdbe735968ac002792a720f0ba4faca6
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/lorewar2/bio_exp
[INFO] finished tweaking git repo https://github.com/lorewar2/bio_exp
[INFO] tweaked toml for git repo https://github.com/lorewar2/bio_exp written to /workspace/builds/worker-3-tc1/source/Cargo.toml
[INFO] crate git repo https://github.com/lorewar2/bio_exp 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" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]      Locking 137 packages to latest compatible versions
[INFO] [stderr]       Adding aho-corasick v1.1.3
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[INFO] [stderr]       Adding cc v1.1.15
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[INFO] [stderr]       Adding curl-sys v0.4.74+curl-8.9.0
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[INFO] [stderr]  Downloading crates ...
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 7c7005552aaa635f3010fb3ec1c7c1c1b0b35df06f100c5b960277cffc98fe3d
[INFO] running `Command { std: "docker" "start" "-a" "7c7005552aaa635f3010fb3ec1c7c1c1b0b35df06f100c5b960277cffc98fe3d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "7c7005552aaa635f3010fb3ec1c7c1c1b0b35df06f100c5b960277cffc98fe3d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "7c7005552aaa635f3010fb3ec1c7c1c1b0b35df06f100c5b960277cffc98fe3d", kill_on_drop: false }`
[INFO] [stdout] 7c7005552aaa635f3010fb3ec1c7c1c1b0b35df06f100c5b960277cffc98fe3d
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] ac690a7323da7580887b195ae79a0da87de748726fb2fd2c214d537ee408b8da
[INFO] running `Command { std: "docker" "start" "-a" "ac690a7323da7580887b195ae79a0da87de748726fb2fd2c214d537ee408b8da", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.158
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[INFO] [stderr]    Compiling libm v0.2.8
[INFO] [stderr]    Compiling glob v0.3.1
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[INFO] [stderr]    Compiling paste v1.0.15
[INFO] [stderr]     Checking memchr v2.7.4
[INFO] [stderr]    Compiling minimal-lexical v0.2.1
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling matrixmultiply v0.3.9
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[INFO] [stderr]    Compiling serde v1.0.209
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[INFO] [stderr]    Compiling bindgen v0.69.4
[INFO] [stderr]    Compiling syn v2.0.76
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[INFO] [stderr]    Compiling syn v1.0.109
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[INFO] [stderr]    Compiling rustc_version v0.1.7
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[INFO] [stderr]    Compiling bv v0.11.1
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[INFO] [stderr]     Checking bit-vec v0.8.0
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[INFO] [stderr]     Checking num-complex v0.4.6
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[INFO] [stderr]     Checking num-rational v0.4.2
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[INFO] [stderr]     Checking idna v0.5.0
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking strum v0.26.3
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[INFO] [stderr]    Compiling openssl-src v300.3.1+3.3.1
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[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
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[INFO] [stderr]    Compiling serde_derive v1.0.209
[INFO] [stderr]    Compiling thiserror-impl v1.0.63
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[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling nalgebra-macros v0.2.2
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[INFO] [stderr]     Checking ppv-lite86 v0.2.20
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[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking nalgebra v0.32.6
[INFO] [stderr]     Checking nalgebra v0.29.0
[INFO] [stderr]    Compiling hts-sys v2.1.4
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking multimap v0.10.0
[INFO] [stderr]     Checking csv v1.3.0
[INFO] [stderr]     Checking statrs v0.17.1
[INFO] [stderr]     Checking bio v2.0.1
[INFO] [stderr]     Checking statrs v0.16.1
[INFO] [stderr]     Checking rust-htslib v0.47.0
[INFO] [stderr]     Checking bio_exp v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `crate::misc::calculate_deep_quality`
[INFO] [stdout]  --> src/main.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use crate::misc::calculate_deep_quality;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::misc::calculate_deep_quality`
[INFO] [stdout]  --> src/main.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use crate::misc::calculate_deep_quality;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `total` is assigned to, but never used
[INFO] [stdout]   --> src/main.rs:49:21
[INFO] [stdout]    |
[INFO] [stdout] 49 |             let mut total = 0;
[INFO] [stdout]    |                     ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_total` instead
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `hets`
[INFO] [stdout]   --> src/main.rs:50:21
[INFO] [stdout]    |
[INFO] [stdout] 50 |             let mut hets = 0;
[INFO] [stdout]    |                     ^^^^ help: if this is intentional, prefix it with an underscore: `_hets`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `total` is assigned to, but never used
[INFO] [stdout]   --> src/main.rs:49:21
[INFO] [stdout]    |
[INFO] [stdout] 49 |             let mut total = 0;
[INFO] [stdout]    |                     ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_total` instead
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]   --> src/main.rs:51:18
[INFO] [stdout]    |
[INFO] [stdout] 51 |             for (i, _rec) in vcf_reader.records().enumerate() {
[INFO] [stdout]    |                  ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `pos`
[INFO] [stdout]   --> src/main.rs:54:21
[INFO] [stdout]    |
[INFO] [stdout] 54 |                 let pos = rec.pos();
[INFO] [stdout]    |                     ^^^ help: if this is intentional, prefix it with an underscore: `_pos`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `hets`
[INFO] [stdout]   --> src/main.rs:50:21
[INFO] [stdout]    |
[INFO] [stdout] 50 |             let mut hets = 0;
[INFO] [stdout]    |                     ^^^^ help: if this is intentional, prefix it with an underscore: `_hets`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `rec_chrom`
[INFO] [stdout]   --> src/main.rs:61:21
[INFO] [stdout]    |
[INFO] [stdout] 61 |                 let rec_chrom = rec.rid().expect("could not unwrap vcf record id");
[INFO] [stdout]    |                     ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_rec_chrom`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]   --> src/main.rs:51:18
[INFO] [stdout]    |
[INFO] [stdout] 51 |             for (i, _rec) in vcf_reader.records().enumerate() {
[INFO] [stdout]    |                  ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `genotype`
[INFO] [stdout]   --> src/main.rs:63:21
[INFO] [stdout]    |
[INFO] [stdout] 63 |                 let genotype = genotypes.get(0); // assume only 1 and get the first one
[INFO] [stdout]    |                     ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_genotype`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `pos`
[INFO] [stdout]   --> src/main.rs:54:21
[INFO] [stdout]    |
[INFO] [stdout] 54 |                 let pos = rec.pos();
[INFO] [stdout]    |                     ^^^ help: if this is intentional, prefix it with an underscore: `_pos`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `rec_chrom`
[INFO] [stdout]   --> src/main.rs:61:21
[INFO] [stdout]    |
[INFO] [stdout] 61 |                 let rec_chrom = rec.rid().expect("could not unwrap vcf record id");
[INFO] [stdout]    |                     ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_rec_chrom`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `genotype`
[INFO] [stdout]   --> src/main.rs:63:21
[INFO] [stdout]    |
[INFO] [stdout] 63 |                 let genotype = genotypes.get(0); // assume only 1 and get the first one
[INFO] [stdout]    |                     ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_genotype`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/main.rs:50:17
[INFO] [stdout]    |
[INFO] [stdout] 50 |             let mut hets = 0;
[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: variable does not need to be mutable
[INFO] [stdout]   --> src/main.rs:50:17
[INFO] [stdout]    |
[INFO] [stdout] 50 |             let mut hets = 0;
[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: 8 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 8 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 56.83s
[INFO] running `Command { std: "docker" "inspect" "ac690a7323da7580887b195ae79a0da87de748726fb2fd2c214d537ee408b8da", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ac690a7323da7580887b195ae79a0da87de748726fb2fd2c214d537ee408b8da", kill_on_drop: false }`
[INFO] [stdout] ac690a7323da7580887b195ae79a0da87de748726fb2fd2c214d537ee408b8da