[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 try#d990716b6a1fdde1300748828a9c9e79dfd0b898 for pr-74846 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2FGFAtoVCF" "/workspace/builds/worker-5/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-5/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/HopedWall/GFAtoVCF on toolchain d990716b6a1fdde1300748828a9c9e79dfd0b898 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+d990716b6a1fdde1300748828a9c9e79dfd0b898" "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-5/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" "+d990716b6a1fdde1300748828a9c9e79dfd0b898" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Updating git repository `https://github.com/chfi/rs-3-edge` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded gfa v0.2.3 [INFO] [stderr] Downloaded handlegraph v0.2.0 [INFO] [stderr] Downloaded priority-queue v1.0.0 [INFO] [stderr] Downloaded gfa v0.5.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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" "+d990716b6a1fdde1300748828a9c9e79dfd0b898" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 04a846acbb1d0492c4db4a88f30e6b8c6e660fc46ca8f97b99647f2e8ccbd5e6 [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" "04a846acbb1d0492c4db4a88f30e6b8c6e660fc46ca8f97b99647f2e8ccbd5e6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "04a846acbb1d0492c4db4a88f30e6b8c6e660fc46ca8f97b99647f2e8ccbd5e6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "04a846acbb1d0492c4db4a88f30e6b8c6e660fc46ca8f97b99647f2e8ccbd5e6", kill_on_drop: false }` [INFO] [stdout] 04a846acbb1d0492c4db4a88f30e6b8c6e660fc46ca8f97b99647f2e8ccbd5e6 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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" "+d990716b6a1fdde1300748828a9c9e79dfd0b898" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 37e804cf0578f685c2912bc3ee7012152fbcd270a7ecd8fd655f52e45cf82fdd [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" "37e804cf0578f685c2912bc3ee7012152fbcd270a7ecd8fd655f52e45cf82fdd", kill_on_drop: false }` [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Compiling autocfg v1.0.0 [INFO] [stderr] Compiling memchr v2.3.3 [INFO] [stderr] Compiling libc v0.2.71 [INFO] [stderr] Compiling unicode-xid v0.2.1 [INFO] [stderr] Compiling byteorder v1.3.4 [INFO] [stderr] Checking regex-syntax v0.6.18 [INFO] [stderr] Compiling syn v1.0.36 [INFO] [stderr] Compiling lexical-core v0.7.4 [INFO] [stderr] Checking static_assertions v1.1.0 [INFO] [stderr] Checking arrayvec v0.5.1 [INFO] [stderr] Checking fixedbitset v0.2.0 [INFO] [stderr] Checking json v0.12.4 [INFO] [stderr] Checking thread_local v1.0.1 [INFO] [stderr] Checking log v0.4.11 [INFO] [stderr] Compiling proc-macro2 v1.0.19 [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 aho-corasick v0.7.13 [INFO] [stderr] Compiling quote v1.0.7 [INFO] [stderr] Checking regex-automata v0.1.9 [INFO] [stderr] Checking bstr v0.2.13 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking time v0.1.43 [INFO] [stderr] Checking clap v2.33.1 [INFO] [stderr] Checking petgraph v0.5.1 [INFO] [stderr] Checking chrono v0.4.11 [INFO] [stderr] Checking regex v1.3.9 [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 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::>(); [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_neighbors` [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::>(); [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; [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; [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, handle_to_component : &mut Handle2Component) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 6 warnings emitted [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; [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; [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, 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 51.72s [INFO] running `Command { std: "docker" "inspect" "37e804cf0578f685c2912bc3ee7012152fbcd270a7ecd8fd655f52e45cf82fdd", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "37e804cf0578f685c2912bc3ee7012152fbcd270a7ecd8fd655f52e45cf82fdd", kill_on_drop: false }` [INFO] [stdout] 37e804cf0578f685c2912bc3ee7012152fbcd270a7ecd8fd655f52e45cf82fdd