[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] 8a58aacf86bb1e4834bdee720cca29afc224992d
[INFO] documenting bluenote-1577/haplotype_phaser against beta-2020-08-29 for beta-1.47-rustdoc-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fhaplotype_phaser" "/workspace/builds/worker-7/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-7/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/bluenote-1577/haplotype_phaser on toolchain beta-2020-08-29
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-08-29" "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-7/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" "+beta-2020-08-29" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded statrs v0.13.0
[INFO] [stderr]   Downloaded memoffset v0.5.5
[INFO] [stderr]   Downloaded rayon v1.3.1
[INFO] [stderr]   Downloaded bio-types v0.7.0
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded permute v0.1.0
[INFO] [stderr]   Downloaded custom_derive v0.1.7
[INFO] [stderr]   Downloaded rayon-core v1.7.1
[INFO] [stderr]   Downloaded glob v0.3.0
[INFO] [stderr]   Downloaded libz-sys v1.1.0
[INFO] [stderr]   Downloaded rust-htslib v0.32.0
[INFO] [stderr]   Downloaded hts-sys v1.10.3
[INFO] [stderr]   Downloaded num-rational v0.2.4
[INFO] [stderr]   Downloaded linear-map v1.2.0
[INFO] [stderr]   Downloaded bzip2-sys v0.1.9+1.0.8
[INFO] [stderr]   Downloaded lzma-sys v0.1.16
[INFO] [stderr]   Downloaded thiserror-impl v1.0.20
[INFO] [stderr]   Downloaded thiserror v1.0.20
[INFO] [stderr]   Downloaded ieee754 v0.2.6
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded alga v0.9.3
[INFO] [stderr]   Downloaded libm v0.2.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/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" "+beta-2020-08-29" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] d978ab08c45dbdae7605c6d8dca4825f26f4d69ec4e2105c330294ed24a3c2ab
[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" "d978ab08c45dbdae7605c6d8dca4825f26f4d69ec4e2105c330294ed24a3c2ab", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "d978ab08c45dbdae7605c6d8dca4825f26f4d69ec4e2105c330294ed24a3c2ab", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d978ab08c45dbdae7605c6d8dca4825f26f4d69ec4e2105c330294ed24a3c2ab", kill_on_drop: false }`
[INFO] [stdout] d978ab08c45dbdae7605c6d8dca4825f26f4d69ec4e2105c330294ed24a3c2ab
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/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" "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" "rustops/crates-build-env@sha256:d92eaeed33fa75130ca1ee6c8a01d1ffb62bac859dfdfb3450e3e5d1c0146529" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-08-29" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] [stdout] 57115fe631e2c9699060ab1ddf610e5264ffa11a91be3ce00d31be69c42f1f92
[INFO] running `Command { std: "docker" "start" "-a" "57115fe631e2c9699060ab1ddf610e5264ffa11a91be3ce00d31be69c42f1f92", kill_on_drop: false }`
[INFO] [stderr]     Checking cfg-if v0.1.10
[INFO] [stderr]    Compiling syn v1.0.38
[INFO] [stderr]     Checking lazy_static v1.4.0
[INFO] [stderr]     Checking ppv-lite86 v0.2.9
[INFO] [stderr]     Checking tinyvec v0.3.4
[INFO] [stderr]     Checking matches v0.1.8
[INFO] [stderr]     Checking scopeguard v1.1.0
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]     Checking regex-syntax v0.6.18
[INFO] [stderr]     Checking percent-encoding v2.1.0
[INFO] [stderr]     Checking unicode-width v0.1.8
[INFO] [stderr]     Checking quick-error v1.2.3
[INFO] [stderr]     Checking ansi_term v0.11.0
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking strsim v0.8.0
[INFO] [stderr]     Checking either v1.6.0
[INFO] [stderr]     Checking permute v0.1.0
[INFO] [stderr]    Compiling libc v0.2.74
[INFO] [stderr]    Compiling libm v0.2.1
[INFO] [stderr]    Compiling num-traits v0.2.12
[INFO] [stderr]    Compiling getrandom v0.1.14
[INFO] [stderr]    Compiling maybe-uninit v2.0.0
[INFO] [stderr]    Compiling memchr v2.3.3
[INFO] [stderr]    Compiling typenum v1.12.0
[INFO] [stderr]    Compiling rayon-core v1.7.1
[INFO] [stderr]    Compiling byteorder v1.3.4
[INFO] [stderr]    Compiling bitflags v1.2.1
[INFO] [stderr]    Compiling serde v1.0.115
[INFO] [stderr]     Checking matrixmultiply v0.2.3
[INFO] [stderr]     Checking unicode-bidi v0.3.4
[INFO] [stderr]     Checking textwrap v0.11.0
[INFO] [stderr]    Compiling standback v0.2.9
[INFO] [stderr]    Compiling crossbeam-utils v0.7.2
[INFO] [stderr]    Compiling crossbeam-epoch v0.8.2
[INFO] [stderr]    Compiling num-complex v0.2.4
[INFO] [stderr]    Compiling memoffset v0.5.5
[INFO] [stderr]    Compiling num-integer v0.1.43
[INFO] [stderr]    Compiling num-rational v0.2.4
[INFO] [stderr]    Compiling time v0.2.16
[INFO] [stderr]    Compiling rayon v1.3.1
[INFO] [stderr]     Checking thread_local v1.0.1
[INFO] [stderr]    Compiling jobserver v0.1.21
[INFO] [stderr]     Checking unicode-normalization v0.1.13
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling cc v1.0.59
[INFO] [stderr]     Checking aho-corasick v0.7.13
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking num_cpus v1.13.0
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]     Checking crossbeam-queue v0.2.3
[INFO] [stderr]     Checking clap v2.33.3
[INFO] [stderr]     Checking rand_core v0.5.1
[INFO] [stderr]     Checking crossbeam-deque v0.7.3
[INFO] [stderr]     Checking generic-array v0.13.2
[INFO] [stderr]     Checking idna v0.2.0
[INFO] [stderr]    Compiling openssl-src v111.10.2+1.1.1g
[INFO] [stderr]     Checking rand_chacha v0.2.2
[INFO] [stderr]     Checking rand_pcg v0.2.1
[INFO] [stderr]     Checking approx v0.3.2
[INFO] [stderr]    Compiling libz-sys v1.1.0
[INFO] [stderr]    Compiling curl-sys v0.4.36+curl-7.71.1
[INFO] [stderr]    Compiling bzip2-sys v0.1.9+1.0.8
[INFO] [stderr]    Compiling lzma-sys v0.1.16
[INFO] [stderr]    Compiling hts-sys v1.10.3
[INFO] [stderr]     Checking url v2.1.1
[INFO] [stderr]    Compiling openssl-sys v0.9.58
[INFO] [stderr]     Checking rand v0.7.3
[INFO] [stderr]     Checking alga v0.9.3
[INFO] [stderr]     Checking regex v1.3.9
[INFO] [stderr]     Checking rand_distr v0.2.2
[INFO] [stderr]     Checking nalgebra v0.19.0
[INFO] [stderr]    Compiling derive-new v0.5.8
[INFO] [stderr]    Compiling thiserror-impl v1.0.20
[INFO] [stderr]    Compiling serde_derive v1.0.115
[INFO] [stderr]    Compiling time-macros-impl v0.1.1
[INFO] [stderr]     Checking time-macros v0.1.0
[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] [stderr]  Documenting flopp v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `std::time::Instant`
[INFO] [stdout]  --> src/local_clustering.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use std::time::Instant;
[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:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::time::Instant;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 2 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [optimized + debuginfo] target(s) in 4m 00s
[INFO] running `Command { std: "docker" "inspect" "57115fe631e2c9699060ab1ddf610e5264ffa11a91be3ce00d31be69c42f1f92", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "57115fe631e2c9699060ab1ddf610e5264ffa11a91be3ce00d31be69c42f1f92", kill_on_drop: false }`
[INFO] [stdout] 57115fe631e2c9699060ab1ddf610e5264ffa11a91be3ce00d31be69c42f1f92