[INFO] cloning repository https://github.com/HopedWall/GFAtoVCF
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/HopedWall/GFAtoVCF" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2FGFAtoVCF", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2FGFAtoVCF'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 729713d301a6a330b62573d464e375c44a65efd1
[INFO] checking HopedWall/GFAtoVCF against beta-2020-07-24 for pr-75494-beta
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2FGFAtoVCF" "/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/HopedWall/GFAtoVCF on toolchain beta-2020-07-24
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-07-24" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/HopedWall/GFAtoVCF
[INFO] finished tweaking git repo https://github.com/HopedWall/GFAtoVCF
[INFO] tweaked toml for git repo https://github.com/HopedWall/GFAtoVCF written to /workspace/builds/worker-4/source/Cargo.toml
[INFO] crate git repo https://github.com/HopedWall/GFAtoVCF already has a lockfile, it will not be regenerated
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-07-24" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[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" "rustops/crates-build-env@sha256:a636fd89d022f18117e1dc8fb37a0a009933cdbbe082814857f0e2024962d47c" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-07-24" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] adf372adba4d90c2e64b570a5ffe54fe97ca18f7d67d8fb4591a7d9c66ed6814
[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" "adf372adba4d90c2e64b570a5ffe54fe97ca18f7d67d8fb4591a7d9c66ed6814", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "adf372adba4d90c2e64b570a5ffe54fe97ca18f7d67d8fb4591a7d9c66ed6814", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "adf372adba4d90c2e64b570a5ffe54fe97ca18f7d67d8fb4591a7d9c66ed6814", kill_on_drop: false }`
[INFO] [stdout] adf372adba4d90c2e64b570a5ffe54fe97ca18f7d67d8fb4591a7d9c66ed6814
[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=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:a636fd89d022f18117e1dc8fb37a0a009933cdbbe082814857f0e2024962d47c" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-07-24" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 88425b51180fa1972247b7e0cc7409e0972628edd6e8eee74b70f57a571ce44e
[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" "88425b51180fa1972247b7e0cc7409e0972628edd6e8eee74b70f57a571ce44e", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]    Compiling version_check v0.9.2
[INFO] [stderr]    Compiling autocfg v1.0.0
[INFO] [stderr]    Compiling memchr v2.3.3
[INFO] [stderr]     Checking lazy_static v1.4.0
[INFO] [stderr]    Compiling bitflags v1.2.1
[INFO] [stderr]    Compiling proc-macro2 v1.0.19
[INFO] [stderr]    Compiling unicode-xid v0.2.1
[INFO] [stderr]    Compiling byteorder v1.3.4
[INFO] [stderr]    Compiling ryu v1.0.5
[INFO] [stderr]     Checking regex-syntax v0.6.18
[INFO] [stderr]     Checking cfg-if v0.1.10
[INFO] [stderr]    Compiling lexical-core v0.7.4
[INFO] [stderr]     Checking arrayvec v0.5.1
[INFO] [stderr]     Checking unicode-width v0.1.7
[INFO] [stderr]     Checking strsim v0.8.0
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking ansi_term v0.11.0
[INFO] [stderr]    Compiling log v0.4.11
[INFO] [stderr]     Checking json v0.12.4
[INFO] [stderr]     Checking thread_local v1.0.1
[INFO] [stderr]     Checking textwrap v0.11.0
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]     Checking time v0.1.43
[INFO] [stderr]     Checking aho-corasick v0.7.13
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling nom v5.1.2
[INFO] [stderr]    Compiling indexmap v1.4.0
[INFO] [stderr]    Compiling num-traits v0.2.12
[INFO] [stderr]    Compiling num-integer v0.1.43
[INFO] [stderr]    Compiling priority-queue v1.0.0
[INFO] [stderr]     Checking clap v2.33.1
[INFO] [stderr]     Checking regex-automata v0.1.9
[INFO] [stderr]     Checking bstr v0.2.13
[INFO] [stderr]    Compiling quote v1.0.7
[INFO] [stderr]     Checking petgraph v0.5.1
[INFO] [stderr]    Compiling syn v1.0.36
[INFO] [stderr]     Checking regex v1.3.9
[INFO] [stderr]     Checking chrono v0.4.11
[INFO] [stderr]     Checking gfa v0.5.0
[INFO] [stderr]     Checking gfa v0.2.3
[INFO] [stderr]     Checking handlegraph v0.2.0
[INFO] [stderr]    Compiling structopt-derive v0.4.8
[INFO] [stderr]     Checking structopt v0.3.15
[INFO] [stderr]     Checking three-edge-connected v0.1.0 (https://github.com/chfi/rs-3-edge#d2b6e5a4)
[INFO] [stderr]     Checking gfa_to_vcf v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `crate::snarl_detection::*`
[INFO] [stdout]   --> src/main.rs:27:5
[INFO] [stdout]    |
[INFO] [stdout] 27 | use crate::snarl_detection::*;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `component`
[INFO] [stdout]    --> src/bubble_detection.rs:331:9
[INFO] [stdout]     |
[INFO] [stdout] 331 |     for component in connected_components {
[INFO] [stdout]     |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_component`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `neighbors`
[INFO] [stdout]    --> src/bubble_detection.rs:341:17
[INFO] [stdout]     |
[INFO] [stdout] 341 |             let neighbors = handle_edges_iter(graph, handle, Direction::Right).map(|x| x.id()).collect::<Vec<NodeId>>();
[INFO] [stdout]     |                 ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_neighbors`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::snarl_detection::*`
[INFO] [stdout]   --> src/main.rs:27:5
[INFO] [stdout]    |
[INFO] [stdout] 27 | use crate::snarl_detection::*;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type alias is never used: `HandleSet`
[INFO] [stdout]  --> src/snarl_detection.rs:8:1
[INFO] [stdout]   |
[INFO] [stdout] 8 | type HandleSet = HashSet<Handle>;
[INFO] [stdout]   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type alias is never used: `Handle2Component`
[INFO] [stdout]  --> src/snarl_detection.rs:9:1
[INFO] [stdout]   |
[INFO] [stdout] 9 | type Handle2Component = HashMap<Handle, usize>;
[INFO] [stdout]   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `compute_side_components`
[INFO] [stdout]   --> src/snarl_detection.rs:12:4
[INFO] [stdout]    |
[INFO] [stdout] 12 | fn compute_side_components(graph : &HashGraph, components : &mut Vec<HandleSet>, handle_to_component : &mut Handle2Component) {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 6 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `component`
[INFO] [stdout]    --> src/bubble_detection.rs:331:9
[INFO] [stdout]     |
[INFO] [stdout] 331 |     for component in connected_components {
[INFO] [stdout]     |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_component`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `neighbors`
[INFO] [stdout]    --> src/bubble_detection.rs:341:17
[INFO] [stdout]     |
[INFO] [stdout] 341 |             let neighbors = handle_edges_iter(graph, handle, Direction::Right).map(|x| x.id()).collect::<Vec<NodeId>>();
[INFO] [stdout]     |                 ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_neighbors`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type alias is never used: `HandleSet`
[INFO] [stdout]  --> src/snarl_detection.rs:8:1
[INFO] [stdout]   |
[INFO] [stdout] 8 | type HandleSet = HashSet<Handle>;
[INFO] [stdout]   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type alias is never used: `Handle2Component`
[INFO] [stdout]  --> src/snarl_detection.rs:9:1
[INFO] [stdout]   |
[INFO] [stdout] 9 | type Handle2Component = HashMap<Handle, usize>;
[INFO] [stdout]   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `compute_side_components`
[INFO] [stdout]   --> src/snarl_detection.rs:12:4
[INFO] [stdout]    |
[INFO] [stdout] 12 | fn compute_side_components(graph : &HashGraph, components : &mut Vec<HandleSet>, handle_to_component : &mut Handle2Component) {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 6 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 42.91s
[INFO] running `Command { std: "docker" "inspect" "88425b51180fa1972247b7e0cc7409e0972628edd6e8eee74b70f57a571ce44e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "88425b51180fa1972247b7e0cc7409e0972628edd6e8eee74b70f57a571ce44e", kill_on_drop: false }`
[INFO] [stdout] 88425b51180fa1972247b7e0cc7409e0972628edd6e8eee74b70f57a571ce44e
