[INFO] cloning repository https://github.com/Fede-Berga/Variation_Graph [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/Fede-Berga/Variation_Graph" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FFede-Berga%2FVariation_Graph", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FFede-Berga%2FVariation_Graph'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] eac6b8765d4251ade1080a40678b8d3ce4d1109a [INFO] testing Fede-Berga/Variation_Graph against 1.60.0 for beta-1.61-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FFede-Berga%2FVariation_Graph" "/workspace/builds/worker-0/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-0/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/Fede-Berga/Variation_Graph on toolchain 1.60.0 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.60.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/Fede-Berga/Variation_Graph [INFO] finished tweaking git repo https://github.com/Fede-Berga/Variation_Graph [INFO] tweaked toml for git repo https://github.com/Fede-Berga/Variation_Graph written to /workspace/builds/worker-0/source/Cargo.toml [INFO] crate git repo https://github.com/Fede-Berga/Variation_Graph already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.60.0" "fetch" "--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-handlegraph` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded bio-types v0.11.0 [INFO] [stderr] Downloaded triple_accel v0.3.4 [INFO] [stderr] Downloaded statrs v0.13.0 [INFO] [stderr] Downloaded bio v0.34.0 [INFO] [stderr] Downloaded wyhash v0.5.0 [INFO] [stderr] Downloaded gfa v0.10.0 [INFO] [stderr] Downloaded boomphf v0.5.9 [INFO] [stderr] Downloaded succinct v0.5.2 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/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:eaef2f80f755933c374d2ae5edccceec0c1312ceb8a4e0b6404e8ab76561e1e5" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "metadata" "--no-deps" "--format-version=1", 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] c67d3a9cb37d5bb0a605c985dd323f6282a811c71e5b2b61881e4d59993b9b5d [INFO] running `Command { std: "docker" "start" "-a" "c67d3a9cb37d5bb0a605c985dd323f6282a811c71e5b2b61881e4d59993b9b5d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "c67d3a9cb37d5bb0a605c985dd323f6282a811c71e5b2b61881e4d59993b9b5d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "c67d3a9cb37d5bb0a605c985dd323f6282a811c71e5b2b61881e4d59993b9b5d", kill_on_drop: false }` [INFO] [stdout] c67d3a9cb37d5bb0a605c985dd323f6282a811c71e5b2b61881e4d59993b9b5d [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/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:eaef2f80f755933c374d2ae5edccceec0c1312ceb8a4e0b6404e8ab76561e1e5" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "build" "--frozen" "--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] 2957ee81a0634c878f50c97d4129ef84dc1bc725e0e54eef66b96797caaa4a26 [INFO] running `Command { std: "docker" "start" "-a" "2957ee81a0634c878f50c97d4129ef84dc1bc725e0e54eef66b96797caaa4a26", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling syn v1.0.72 [INFO] [stderr] Compiling libc v0.2.95 [INFO] [stderr] Compiling serde v1.0.126 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling rand_core v0.6.2 [INFO] [stderr] Compiling ndarray v0.14.0 [INFO] [stderr] Compiling array-macro v1.0.5 [INFO] [stderr] Compiling bio v0.34.0 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling bytecount v0.6.2 [INFO] [stderr] Compiling triple_accel v0.3.4 [INFO] [stderr] Compiling strum v0.20.0 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling num-rational v0.2.4 [INFO] [stderr] Compiling indexmap v1.6.2 [INFO] [stderr] Compiling matrixmultiply v0.2.4 [INFO] [stderr] Compiling csv-core v0.1.10 [INFO] [stderr] Compiling generic-array v0.13.3 [INFO] [stderr] Compiling approx v0.3.2 [INFO] [stderr] Compiling num-complex v0.3.1 [INFO] [stderr] Compiling ordered-float v1.1.1 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling succinct v0.5.2 [INFO] [stderr] Compiling wyhash v0.5.0 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling petgraph v0.5.1 [INFO] [stderr] Compiling getrandom v0.1.16 [INFO] [stderr] Compiling num_cpus v1.13.0 [INFO] [stderr] Compiling memmap v0.7.0 [INFO] [stderr] Compiling alga v0.9.3 [INFO] [stderr] Compiling rand_core v0.5.1 [INFO] [stderr] Compiling rayon-core v1.9.1 [INFO] [stderr] Compiling rand_chacha v0.2.2 [INFO] [stderr] Compiling rand v0.7.3 [INFO] [stderr] Compiling rayon v1.5.1 [INFO] [stderr] Compiling rand_distr v0.2.2 [INFO] [stderr] Compiling nalgebra v0.19.0 [INFO] [stderr] Compiling serde_derive v1.0.126 [INFO] [stderr] Compiling bytemuck_derive v1.0.1 [INFO] [stderr] Compiling thiserror-impl v1.0.25 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling enum-map-derive v0.4.6 [INFO] [stderr] Compiling strum_macros v0.20.1 [INFO] [stderr] Compiling getset v0.0.9 [INFO] [stderr] Compiling boomphf v0.5.9 [INFO] [stderr] Compiling enum-map v0.6.4 [INFO] [stderr] Compiling bytemuck v1.5.1 [INFO] [stderr] Compiling thiserror v1.0.25 [INFO] [stderr] Compiling bio-types v0.11.0 [INFO] [stderr] Compiling bstr v0.2.16 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling multimap v0.8.3 [INFO] [stderr] Compiling csv v1.1.6 [INFO] [stderr] Compiling gfa v0.10.0 [INFO] [stderr] Compiling statrs v0.13.0 [INFO] [stderr] Compiling handlegraph v0.7.0-alpha.7 (https://github.com/chfi/rs-handlegraph#5d44c62c) [INFO] [stderr] Compiling variation_graph v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `Interval` [INFO] [stdout] --> src/alignment_parser.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | Interval, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs` [INFO] [stdout] --> src/multiple_alignment_format/mod.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use std::fs; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `last_node` [INFO] [stdout] --> src/variation_graph.rs:32:5 [INFO] [stdout] | [INFO] [stdout] 32 | last_node : Handle, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] note: `VariationGraph` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] --> src/variation_graph.rs:28:10 [INFO] [stdout] | [INFO] [stdout] 28 | #[derive(Debug)] [INFO] [stdout] | ^^^^^ [INFO] [stdout] = note: this warning originates in the derive macro `Debug` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 3 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 1m 48s [INFO] running `Command { std: "docker" "inspect" "2957ee81a0634c878f50c97d4129ef84dc1bc725e0e54eef66b96797caaa4a26", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "2957ee81a0634c878f50c97d4129ef84dc1bc725e0e54eef66b96797caaa4a26", kill_on_drop: false }` [INFO] [stdout] 2957ee81a0634c878f50c97d4129ef84dc1bc725e0e54eef66b96797caaa4a26 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/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:eaef2f80f755933c374d2ae5edccceec0c1312ceb8a4e0b6404e8ab76561e1e5" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 8a8d0746aa17847b7fcf157c9302823e90ad47d3459b8ab672fdb817cf6cc469 [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" "8a8d0746aa17847b7fcf157c9302823e90ad47d3459b8ab672fdb817cf6cc469", kill_on_drop: false }` [INFO] [stderr] Compiling variation_graph v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `Interval` [INFO] [stdout] --> src/alignment_parser.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | Interval, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs` [INFO] [stdout] --> src/multiple_alignment_format/mod.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use std::fs; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `last_node` [INFO] [stdout] --> src/variation_graph.rs:32:5 [INFO] [stdout] | [INFO] [stdout] 32 | last_node : Handle, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] note: `VariationGraph` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] --> src/variation_graph.rs:28:10 [INFO] [stdout] | [INFO] [stdout] 28 | #[derive(Debug)] [INFO] [stdout] | ^^^^^ [INFO] [stdout] = note: this warning originates in the derive macro `Debug` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 3 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `VariationGraphError` [INFO] [stdout] --> tests/variation_graph_test.rs:7:39 [INFO] [stdout] | [INFO] [stdout] 7 | variation_graph::{VariationGraph, VariationGraphError}, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `FastaParser` [INFO] [stdout] --> tests/parser_test.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | FastaParser, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0468]: an `extern crate` loading macros must be at the crate root [INFO] [stdout] --> src/multiple_alignment_format/mod.rs:3:1 [INFO] [stdout] | [INFO] [stdout] 3 | extern crate maplit; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `MAFBlock` [INFO] [stdout] --> src/multiple_alignment_format/output.rs:71:9 [INFO] [stdout] | [INFO] [stdout] 71 | use MAFBlock; [INFO] [stdout] | ^^^^^^^^ no external crate `MAFBlock` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `MAFBlockEntry` [INFO] [stdout] --> src/multiple_alignment_format/output.rs:72:9 [INFO] [stdout] | [INFO] [stdout] 72 | use MAFBlockEntry; [INFO] [stdout] | ^^^^^^^^^^^^^ no external crate `MAFBlockEntry` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `MAFBlockAlignedEntry` [INFO] [stdout] --> src/multiple_alignment_format/output.rs:73:9 [INFO] [stdout] | [INFO] [stdout] 73 | use MAFBlockAlignedEntry; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ no external crate `MAFBlockAlignedEntry` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `MAFBlockUnalignedEntry` [INFO] [stdout] --> src/multiple_alignment_format/output.rs:74:9 [INFO] [stdout] | [INFO] [stdout] 74 | use MAFBlockUnalignedEntry; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ no external crate `MAFBlockUnalignedEntry` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `Strand` [INFO] [stdout] --> src/multiple_alignment_format/output.rs:75:9 [INFO] [stdout] | [INFO] [stdout] 75 | use Strand; [INFO] [stdout] | ^^^^^^ no external crate `Strand` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `AlignedContext` [INFO] [stdout] --> src/multiple_alignment_format/output.rs:76:9 [INFO] [stdout] | [INFO] [stdout] 76 | use AlignedContext; [INFO] [stdout] | ^^^^^^^^^^^^^^ no external crate `AlignedContext` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `AlignedContextStatus` [INFO] [stdout] --> src/multiple_alignment_format/output.rs:77:9 [INFO] [stdout] | [INFO] [stdout] 77 | use AlignedContextStatus; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ no external crate `AlignedContextStatus` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `UnalignedContextStatus` [INFO] [stdout] --> src/multiple_alignment_format/output.rs:78:9 [INFO] [stdout] | [INFO] [stdout] 78 | use UnalignedContextStatus; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ no external crate `UnalignedContextStatus` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Interval` [INFO] [stdout] --> src/alignment_parser.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | Interval, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 9 previous errors; 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0468. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] [INFO] [stderr] error: could not compile `variation_graph` due to 10 previous errors; 1 warning emitted [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: build failed [INFO] running `Command { std: "docker" "inspect" "8a8d0746aa17847b7fcf157c9302823e90ad47d3459b8ab672fdb817cf6cc469", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8a8d0746aa17847b7fcf157c9302823e90ad47d3459b8ab672fdb817cf6cc469", kill_on_drop: false }` [INFO] [stdout] 8a8d0746aa17847b7fcf157c9302823e90ad47d3459b8ab672fdb817cf6cc469