[INFO] cloning repository https://github.com/bluenote-1577/haplotype_phaser
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/bluenote-1577/haplotype_phaser" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fhaplotype_phaser", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fhaplotype_phaser'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] bdeca8b9904951e17d4b817ac2a5563de9f9d7c4
[INFO] checking bluenote-1577/haplotype_phaser against try#f47dd4da3ae8c32c9e65d307bfe640b143e674df for pr-77526
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fhaplotype_phaser" "/workspace/builds/worker-8/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-8/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/bluenote-1577/haplotype_phaser on toolchain f47dd4da3ae8c32c9e65d307bfe640b143e674df
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+f47dd4da3ae8c32c9e65d307bfe640b143e674df" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/bluenote-1577/haplotype_phaser
[INFO] finished tweaking git repo https://github.com/bluenote-1577/haplotype_phaser
[INFO] tweaked toml for git repo https://github.com/bluenote-1577/haplotype_phaser written to /workspace/builds/worker-8/source/Cargo.toml
[INFO] crate git repo https://github.com/bluenote-1577/haplotype_phaser already has a lockfile, it will not be regenerated
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+f47dd4da3ae8c32c9e65d307bfe640b143e674df" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-8/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-8/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" "rustops/crates-build-env@sha256:d92eaeed33fa75130ca1ee6c8a01d1ffb62bac859dfdfb3450e3e5d1c0146529" "/opt/rustwide/cargo-home/bin/cargo" "+f47dd4da3ae8c32c9e65d307bfe640b143e674df" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] e3b1a28f233fddf53e58f87fafe6fda0db24120faf0039d7a709898d02a253b6
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] running `Command { std: "docker" "start" "-a" "e3b1a28f233fddf53e58f87fafe6fda0db24120faf0039d7a709898d02a253b6", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "e3b1a28f233fddf53e58f87fafe6fda0db24120faf0039d7a709898d02a253b6", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e3b1a28f233fddf53e58f87fafe6fda0db24120faf0039d7a709898d02a253b6", kill_on_drop: false }`
[INFO] [stdout] e3b1a28f233fddf53e58f87fafe6fda0db24120faf0039d7a709898d02a253b6
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-8/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-8/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" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:d92eaeed33fa75130ca1ee6c8a01d1ffb62bac859dfdfb3450e3e5d1c0146529" "/opt/rustwide/cargo-home/bin/cargo" "+f47dd4da3ae8c32c9e65d307bfe640b143e674df" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] e7e0ce28b2f1ecb01483eee648cb13f3dc5be23d619870753335696de9d09b37
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] running `Command { std: "docker" "start" "-a" "e7e0ce28b2f1ecb01483eee648cb13f3dc5be23d619870753335696de9d09b37", kill_on_drop: false }`
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[INFO] [stderr]     Checking crossbeam-deque v0.7.3
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[INFO] [stderr]    Compiling lzma-sys v0.1.16
[INFO] [stderr]    Compiling bzip2-sys v0.1.9+1.0.8
[INFO] [stderr]    Compiling curl-sys v0.4.36+curl-7.71.1
[INFO] [stderr]    Compiling hts-sys v1.10.3
[INFO] [stderr]     Checking rand v0.7.3
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[INFO] [stderr]    Compiling derive-new v0.5.8
[INFO] [stderr]    Compiling serde_derive v1.0.115
[INFO] [stderr]    Compiling time-macros-impl v0.1.1
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[INFO] [stderr]     Checking thiserror v1.0.20
[INFO] [stderr]     Checking bio-types v0.7.0
[INFO] [stderr]     Checking statrs v0.13.0
[INFO] [stderr]     Checking rust-htslib v0.32.0
[INFO] [stderr]     Checking flopp v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `Binomial`
[INFO] [stdout]  --> src/local_clustering.rs:5:28
[INFO] [stdout]   |
[INFO] [stdout] 5 | use statrs::distribution::{Binomial, ChiSquared, Univariate};
[INFO] [stdout]   |                            ^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::time::Instant`
[INFO] [stdout]   --> src/vcf_polishing.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::time::Instant;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Binomial`
[INFO] [stdout]  --> src/local_clustering.rs:5:28
[INFO] [stdout]   |
[INFO] [stdout] 5 | use statrs::distribution::{Binomial, ChiSquared, Univariate};
[INFO] [stdout]   |                            ^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::time::Instant`
[INFO] [stdout]   --> src/vcf_polishing.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::time::Instant;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `same`
[INFO] [stdout]    --> src/vcf_polishing.rs:330:22
[INFO] [stdout]     |
[INFO] [stdout] 330 |                 let (same,dist) = utils_frags::distance(frag_in_set, frag);
[INFO] [stdout]     |                      ^^^^ help: if this is intentional, prefix it with an underscore: `_same`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `get_best_perms_mec`
[INFO] [stdout]    --> src/vcf_polishing.rs:114:4
[INFO] [stdout]     |
[INFO] [stdout] 114 | fn get_best_perms_mec(part1: &Vec<FxHashSet<&Frag>>, part2: &Vec<FxHashSet<&Frag>>) -> Vec<Vec<usize>> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `get_mec_from_part`
[INFO] [stdout]    --> src/vcf_polishing.rs:232:4
[INFO] [stdout]     |
[INFO] [stdout] 232 | fn get_mec_from_part(part : &Vec<FxHashSet<&Frag>>) -> i32{
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 5 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `same`
[INFO] [stdout]    --> src/vcf_polishing.rs:330:22
[INFO] [stdout]     |
[INFO] [stdout] 330 |                 let (same,dist) = utils_frags::distance(frag_in_set, frag);
[INFO] [stdout]     |                      ^^^^ help: if this is intentional, prefix it with an underscore: `_same`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `get_best_perms_mec`
[INFO] [stdout]    --> src/vcf_polishing.rs:114:4
[INFO] [stdout]     |
[INFO] [stdout] 114 | fn get_best_perms_mec(part1: &Vec<FxHashSet<&Frag>>, part2: &Vec<FxHashSet<&Frag>>) -> Vec<Vec<usize>> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `get_mec_from_part`
[INFO] [stdout]    --> src/vcf_polishing.rs:232:4
[INFO] [stdout]     |
[INFO] [stdout] 232 | fn get_mec_from_part(part : &Vec<FxHashSet<&Frag>>) -> i32{
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 5 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `FxHashMap`
[INFO] [stdout]  --> tests/frag_reader_test.rs:5:24
[INFO] [stdout]   |
[INFO] [stdout] 5 | use fxhash::{FxHashSet,FxHashMap};
[INFO] [stdout]   |                        ^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `HashSet`
[INFO] [stdout]  --> tests/frag_reader_test.rs:6:24
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::collections::{HashSet,BTreeMap};
[INFO] [stdout]   |                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary trailing semicolon
[INFO] [stdout]   --> tests/frag_reader_test.rs:80:48
[INFO] [stdout]    |
[INFO] [stdout] 80 |     let mut hashset_int = FxHashSet::default();;
[INFO] [stdout]    |                                                ^ help: remove this semicolon
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(redundant_semicolons)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `indexed_reads`
[INFO] [stdout]   --> tests/frag_reader_test.rs:47:9
[INFO] [stdout]    |
[INFO] [stdout] 47 |     let indexed_reads = utils_frags::get_all_overlaps(&frags);
[INFO] [stdout]    |         ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_indexed_reads`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 4 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [optimized + debuginfo] target(s) in 5m 20s
[INFO] running `Command { std: "docker" "inspect" "e7e0ce28b2f1ecb01483eee648cb13f3dc5be23d619870753335696de9d09b37", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e7e0ce28b2f1ecb01483eee648cb13f3dc5be23d619870753335696de9d09b37", kill_on_drop: false }`
[INFO] [stdout] e7e0ce28b2f1ecb01483eee648cb13f3dc5be23d619870753335696de9d09b37