[INFO] cloning repository https://github.com/mal2017/csc
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/mal2017/csc" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmal2017%2Fcsc", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmal2017%2Fcsc'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] d03c33ee5c6bc2e7583bd50315cc6203d9f34510
[INFO] testing mal2017/csc against beta-2021-09-08 for beta-1.56-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmal2017%2Fcsc" "/workspace/builds/worker-4/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-4/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/mal2017/csc on toolchain beta-2021-09-08
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2021-09-08" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/mal2017/csc
[INFO] finished tweaking git repo https://github.com/mal2017/csc
[INFO] tweaked toml for git repo https://github.com/mal2017/csc written to /workspace/builds/worker-4/source/Cargo.toml
[INFO] crate git repo https://github.com/mal2017/csc already has a lockfile, it will not be regenerated
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2021-09-08" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating git repository `https://github.com/mal2017/ngslib.git`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded clang-sys v0.22.0
[INFO] [stderr]   Downloaded bio-types v0.4.0
[INFO] [stderr]   Downloaded rust-htslib v0.22.0
[INFO] [stderr]   Downloaded bindgen v0.36.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/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:a89201d6b5b9fd45c15d5952ece0a0129e7e80cb26ec023fd59cf09bc26f1604" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2021-09-08" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] ab79b98973f73d2d2dfdb51b240ba55ff0c436d4e3ea78a8d22d9d42e6e3b830
[INFO] running `Command { std: "docker" "start" "-a" "ab79b98973f73d2d2dfdb51b240ba55ff0c436d4e3ea78a8d22d9d42e6e3b830", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "ab79b98973f73d2d2dfdb51b240ba55ff0c436d4e3ea78a8d22d9d42e6e3b830", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ab79b98973f73d2d2dfdb51b240ba55ff0c436d4e3ea78a8d22d9d42e6e3b830", kill_on_drop: false }`
[INFO] [stdout] ab79b98973f73d2d2dfdb51b240ba55ff0c436d4e3ea78a8d22d9d42e6e3b830
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/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" "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:a89201d6b5b9fd45c15d5952ece0a0129e7e80cb26ec023fd59cf09bc26f1604" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2021-09-08" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] a0d4b0c781d180e3700158518593ed5a38c4eae9d5f2e64d521bb06ecf76821f
[INFO] running `Command { std: "docker" "start" "-a" "a0d4b0c781d180e3700158518593ed5a38c4eae9d5f2e64d521bb06ecf76821f", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.51
[INFO] [stderr]    Compiling cc v1.0.35
[INFO] [stderr]    Compiling syn v0.15.31
[INFO] [stderr]    Compiling memchr v2.2.0
[INFO] [stderr]    Compiling serde v1.0.90
[INFO] [stderr]    Compiling cfg-if v0.1.7
[INFO] [stderr]    Compiling regex v1.1.5
[INFO] [stderr]    Compiling either v1.5.2
[INFO] [stderr]    Compiling regex v0.2.11
[INFO] [stderr]    Compiling arrayvec v0.4.10
[INFO] [stderr]    Compiling bindgen v0.36.1
[INFO] [stderr]    Compiling termcolor v1.0.4
[INFO] [stderr]    Compiling num-complex v0.2.1
[INFO] [stderr]    Compiling byteorder v1.3.1
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]    Compiling num-integer v0.1.39
[INFO] [stderr]    Compiling ndarray v0.12.1
[INFO] [stderr]    Compiling bio v0.25.0
[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling bit-vec v0.5.1
[INFO] [stderr]    Compiling linear-map v1.2.0
[INFO] [stderr]    Compiling bytecount v0.3.2
[INFO] [stderr]    Compiling ieee754 v0.2.6
[INFO] [stderr]    Compiling clang-sys v0.22.0
[INFO] [stderr]    Compiling humantime v1.2.0
[INFO] [stderr]    Compiling regex-syntax v0.5.6
[INFO] [stderr]    Compiling proc-macro2 v0.3.5
[INFO] [stderr]    Compiling unicode-normalization v0.1.8
[INFO] [stderr]    Compiling fs-utils v1.1.0
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling quote v0.6.12
[INFO] [stderr]    Compiling itertools-num v0.1.3
[INFO] [stderr]    Compiling approx v0.3.2
[INFO] [stderr]    Compiling ordered-float v1.0.2
[INFO] [stderr]    Compiling log v0.4.6
[INFO] [stderr]    Compiling crossbeam-utils v0.2.2
[INFO] [stderr]    Compiling bit-set v0.5.1
[INFO] [stderr]    Compiling itertools v0.7.11
[INFO] [stderr]    Compiling itertools v0.6.5
[INFO] [stderr]    Compiling itertools v0.8.0
[INFO] [stderr]    Compiling bv v0.10.0
[INFO] [stderr]    Compiling quote v0.5.2
[INFO] [stderr]    Compiling idna v0.1.5
[INFO] [stderr]    Compiling libloading v0.5.0
[INFO] [stderr]    Compiling bzip2-sys v0.1.7
[INFO] [stderr]    Compiling libz-sys v1.0.25
[INFO] [stderr]    Compiling lzma-sys v0.1.14
[INFO] [stderr]    Compiling fxhash v0.2.1
[INFO] [stderr]    Compiling memchr v1.0.2
[INFO] [stderr]    Compiling atty v0.2.11
[INFO] [stderr]    Compiling which v1.0.5
[INFO] [stderr]    Compiling rand v0.4.6
[INFO] [stderr]    Compiling num_cpus v1.10.0
[INFO] [stderr]    Compiling crossbeam-epoch v0.3.1
[INFO] [stderr]    Compiling nom v3.2.1
[INFO] [stderr]    Compiling url v1.7.2
[INFO] [stderr]    Compiling aho-corasick v0.7.3
[INFO] [stderr]    Compiling aho-corasick v0.6.10
[INFO] [stderr]    Compiling csv-core v0.1.5
[INFO] [stderr]    Compiling crossbeam-deque v0.2.0
[INFO] [stderr]    Compiling rayon-core v1.4.1
[INFO] [stderr]    Compiling rand v0.3.23
[INFO] [stderr]    Compiling statrs v0.9.0
[INFO] [stderr]    Compiling rayon v1.0.3
[INFO] [stderr]    Compiling cexpr v0.2.3
[INFO] [stderr]    Compiling serde_derive v1.0.90
[INFO] [stderr]    Compiling env_logger v0.5.13
[INFO] [stderr]    Compiling vec_map v0.8.1
[INFO] [stderr]    Compiling bio-types v0.4.0
[INFO] [stderr]    Compiling csv v1.0.7
[INFO] [stderr]    Compiling multimap v0.4.0
[INFO] [stderr]    Compiling clap v2.32.0
[INFO] [stderr]    Compiling rust-htslib v0.22.0
[INFO] [stderr]    Compiling ngslib v0.1.0 (https://github.com/mal2017/ngslib.git?tag=0.1.0-alpha.2#b34385bf)
[INFO] [stderr]    Compiling cutsites v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `bio::io::bed::*`
[INFO] [stdout]   --> src/main.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use bio::io::bed::*;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `bio::io::bed::Record`
[INFO] [stdout]   --> src/main.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use bio::io::bed::Record;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]   --> src/main.rs:19:5
[INFO] [stdout]    |
[INFO] [stdout] 19 | use itertools::Itertools;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `ArgGroup`
[INFO] [stdout]   --> src/main.rs:25:26
[INFO] [stdout]    |
[INFO] [stdout] 25 |     use clap::{App, Arg, ArgGroup};
[INFO] [stdout]    |                          ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/main.rs:101:9
[INFO] [stdout]     |
[INFO] [stdout] 101 |     let mut bam = bam::IndexedReader::from_path(bp).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: 5 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 1m 26s
[INFO] running `Command { std: "docker" "inspect" "a0d4b0c781d180e3700158518593ed5a38c4eae9d5f2e64d521bb06ecf76821f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a0d4b0c781d180e3700158518593ed5a38c4eae9d5f2e64d521bb06ecf76821f", kill_on_drop: false }`
[INFO] [stdout] a0d4b0c781d180e3700158518593ed5a38c4eae9d5f2e64d521bb06ecf76821f
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/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" "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:a89201d6b5b9fd45c15d5952ece0a0129e7e80cb26ec023fd59cf09bc26f1604" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2021-09-08" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 1c8e0de7fa3f13f04da4b7ba9a5cf39c6ddf3780ffeefc46647895a59e5015c3
[INFO] running `Command { std: "docker" "start" "-a" "1c8e0de7fa3f13f04da4b7ba9a5cf39c6ddf3780ffeefc46647895a59e5015c3", kill_on_drop: false }`
[INFO] [stderr]    Compiling cutsites v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `bio::io::bed::*`
[INFO] [stdout]   --> src/main.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use bio::io::bed::*;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `bio::io::bed::Record`
[INFO] [stdout]   --> src/main.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use bio::io::bed::Record;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]   --> src/main.rs:19:5
[INFO] [stdout]    |
[INFO] [stdout] 19 | use itertools::Itertools;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `ArgGroup`
[INFO] [stdout]   --> src/main.rs:25:26
[INFO] [stdout]    |
[INFO] [stdout] 25 |     use clap::{App, Arg, ArgGroup};
[INFO] [stdout]    |                          ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/main.rs:101:9
[INFO] [stdout]     |
[INFO] [stdout] 101 |     let mut bam = bam::IndexedReader::from_path(bp).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: 5 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 0.98s
[INFO] running `Command { std: "docker" "inspect" "1c8e0de7fa3f13f04da4b7ba9a5cf39c6ddf3780ffeefc46647895a59e5015c3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "1c8e0de7fa3f13f04da4b7ba9a5cf39c6ddf3780ffeefc46647895a59e5015c3", kill_on_drop: false }`
[INFO] [stdout] 1c8e0de7fa3f13f04da4b7ba9a5cf39c6ddf3780ffeefc46647895a59e5015c3
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/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" "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:a89201d6b5b9fd45c15d5952ece0a0129e7e80cb26ec023fd59cf09bc26f1604" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2021-09-08" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] ac0e54381f051f4bfa5408bd1a7b5fd37d3bd2f603846b4300636083d3d26cfa
[INFO] running `Command { std: "docker" "start" "-a" "ac0e54381f051f4bfa5408bd1a7b5fd37d3bd2f603846b4300636083d3d26cfa", kill_on_drop: false }`
[INFO] [stderr] warning: unused import: `bio::io::bed::*`
[INFO] [stderr]   --> src/main.rs:10:5
[INFO] [stderr]    |
[INFO] [stderr] 10 | use bio::io::bed::*;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `bio::io::bed::Record`
[INFO] [stderr]   --> src/main.rs:11:5
[INFO] [stderr]    |
[INFO] [stderr] 11 | use bio::io::bed::Record;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `itertools::Itertools`
[INFO] [stderr]   --> src/main.rs:19:5
[INFO] [stderr]    |
[INFO] [stderr] 19 | use itertools::Itertools;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `ArgGroup`
[INFO] [stderr]   --> src/main.rs:25:26
[INFO] [stderr]    |
[INFO] [stderr] 25 |     use clap::{App, Arg, ArgGroup};
[INFO] [stderr]    |                          ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/main.rs:101:9
[INFO] [stderr]     |
[INFO] [stderr] 101 |     let mut bam = bam::IndexedReader::from_path(bp).unwrap();
[INFO] [stderr]     |         ----^^^
[INFO] [stderr]     |         |
[INFO] [stderr]     |         help: remove this `mut`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_mut)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: `cutsites` (bin "cutsites" test) generated 5 warnings
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 0.10s
[INFO] [stderr]      Running unittests (/opt/rustwide/target/debug/deps/cutsites-db4f29b4a014d329)
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "ac0e54381f051f4bfa5408bd1a7b5fd37d3bd2f603846b4300636083d3d26cfa", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ac0e54381f051f4bfa5408bd1a7b5fd37d3bd2f603846b4300636083d3d26cfa", kill_on_drop: false }`
[INFO] [stdout] ac0e54381f051f4bfa5408bd1a7b5fd37d3bd2f603846b4300636083d3d26cfa