[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] checking Fede-Berga/Variation_Graph/eac6b8765d4251ade1080a40678b8d3ce4d1109a against master#f609b7e0586f81fefb3523e3e17adf779ac416be for pr-129466-2 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FFede-Berga%2FVariation_Graph" "/workspace/builds/worker-4-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-4-tc1/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/Fede-Berga/Variation_Graph on toolchain f609b7e0586f81fefb3523e3e17adf779ac416be [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+f609b7e0586f81fefb3523e3e17adf779ac416be" "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-4-tc1/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: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+f609b7e0586f81fefb3523e3e17adf779ac416be" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating git repository `https://github.com/chfi/rs-handlegraph` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded succinct v0.5.2 [INFO] [stderr] Downloaded boomphf v0.5.9 [INFO] [stderr] Downloaded enum-map v0.6.4 [INFO] [stderr] Downloaded statrs v0.13.0 [INFO] [stderr] Downloaded ndarray v0.14.0 [INFO] [stderr] Downloaded bio-types v0.11.0 [INFO] [stderr] Downloaded triple_accel v0.3.4 [INFO] [stderr] Downloaded enum-map-derive v0.4.6 [INFO] [stderr] Downloaded gfa v0.10.0 [INFO] [stderr] Downloaded bio v0.34.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/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:ceb6ea022f8a89cebbe621bb4987e73a935bd40dfbb726f832cfff4742a5b95a" "/opt/rustwide/cargo-home/bin/cargo" "+f609b7e0586f81fefb3523e3e17adf779ac416be" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 9b956686824a5f743e65a474390f49c15f2968c2e77f1c2982fd391edaf379bb [INFO] running `Command { std: "docker" "start" "-a" "9b956686824a5f743e65a474390f49c15f2968c2e77f1c2982fd391edaf379bb", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "9b956686824a5f743e65a474390f49c15f2968c2e77f1c2982fd391edaf379bb", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9b956686824a5f743e65a474390f49c15f2968c2e77f1c2982fd391edaf379bb", kill_on_drop: false }` [INFO] [stdout] 9b956686824a5f743e65a474390f49c15f2968c2e77f1c2982fd391edaf379bb [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/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" "RUSTDOCFLAGS=--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" "ghcr.io/rust-lang/crates-build-env/linux@sha256:ceb6ea022f8a89cebbe621bb4987e73a935bd40dfbb726f832cfff4742a5b95a" "/opt/rustwide/cargo-home/bin/cargo" "+f609b7e0586f81fefb3523e3e17adf779ac416be" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 76cbaa372c3b8b92383e0823285e20a942caba40ceb209be33bf6965a6e123d4 [INFO] running `Command { std: "docker" "start" "-a" "76cbaa372c3b8b92383e0823285e20a942caba40ceb209be33bf6965a6e123d4", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling proc-macro2 v1.0.27 [INFO] [stderr] Compiling unicode-xid v0.2.2 [INFO] [stderr] Compiling syn v1.0.72 [INFO] [stderr] Compiling libc v0.2.95 [INFO] [stderr] Compiling libm v0.2.1 [INFO] [stderr] Compiling memchr v2.4.0 [INFO] [stderr] Compiling serde_derive v1.0.126 [INFO] [stderr] Compiling serde v1.0.126 [INFO] [stderr] Compiling getrandom v0.1.16 [INFO] [stderr] Compiling crossbeam-utils v0.8.5 [INFO] [stderr] Compiling ryu v1.0.5 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling memoffset v0.6.4 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling crossbeam-epoch v0.9.5 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling typenum v1.13.0 [INFO] [stderr] Compiling quote v1.0.9 [INFO] [stderr] Compiling rayon-core v1.9.1 [INFO] [stderr] Checking ppv-lite86 v0.2.10 [INFO] [stderr] Checking scopeguard v1.1.0 [INFO] [stderr] Checking rand_core v0.5.1 [INFO] [stderr] Checking aho-corasick v0.7.18 [INFO] [stderr] Compiling num-rational v0.2.4 [INFO] [stderr] Compiling lexical-core v0.7.6 [INFO] [stderr] Checking rand_chacha v0.2.2 [INFO] [stderr] Checking either v1.6.1 [INFO] [stderr] Checking regex-automata v0.1.10 [INFO] [stderr] Compiling version_check v0.9.3 [INFO] [stderr] Compiling anyhow v1.0.40 [INFO] [stderr] Checking regex-syntax v0.6.25 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Checking matrixmultiply v0.2.4 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Compiling nom v5.1.2 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Checking rand v0.7.3 [INFO] [stderr] Checking crossbeam-deque v0.8.0 [INFO] [stderr] Checking num_cpus v1.13.0 [INFO] [stderr] Checking crossbeam-channel v0.5.1 [INFO] [stderr] Compiling indexmap v1.6.2 [INFO] [stderr] Compiling rayon v1.5.1 [INFO] [stderr] Compiling unicode-segmentation v1.7.1 [INFO] [stderr] Compiling log v0.4.14 [INFO] [stderr] Checking arrayvec v0.5.2 [INFO] [stderr] Checking alga v0.9.3 [INFO] [stderr] Checking generic-array v0.13.3 [INFO] [stderr] Compiling heck v0.3.3 [INFO] [stderr] Checking rand_distr v0.2.2 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking rand_core v0.6.2 [INFO] [stderr] Checking hashbrown v0.9.1 [INFO] [stderr] Compiling ndarray v0.14.0 [INFO] [stderr] Checking wyhash v0.5.0 [INFO] [stderr] Checking nalgebra v0.19.0 [INFO] [stderr] Checking num-complex v0.3.1 [INFO] [stderr] Checking memmap v0.7.0 [INFO] [stderr] Checking csv-core v0.1.10 [INFO] [stderr] Checking regex v1.5.4 [INFO] [stderr] Checking fixedbitset v0.2.0 [INFO] [stderr] Checking itoa v0.4.7 [INFO] [stderr] Checking bit-vec v0.6.3 [INFO] [stderr] Compiling bio v0.34.0 [INFO] [stderr] Checking array-macro v1.0.5 [INFO] [stderr] Checking bit-set v0.5.2 [INFO] [stderr] Checking petgraph v0.5.1 [INFO] [stderr] Checking succinct v0.5.2 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking ordered-float v1.1.1 [INFO] [stderr] Checking itertools v0.9.0 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking triple_accel v0.3.4 [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] Checking bytemuck v1.5.1 [INFO] [stderr] Compiling strum_macros v0.20.1 [INFO] [stderr] Compiling enum-map-derive v0.4.6 [INFO] [stderr] Checking boomphf v0.5.9 [INFO] [stderr] Compiling getset v0.0.9 [INFO] [stderr] Checking thiserror v1.0.25 [INFO] [stderr] Checking bytecount v0.6.2 [INFO] [stderr] Checking enum-map v0.6.4 [INFO] [stderr] Checking strum v0.20.0 [INFO] [stderr] Checking maplit v1.0.2 [INFO] [stderr] Checking bio-types v0.11.0 [INFO] [stderr] Checking bstr v0.2.16 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking bv v0.11.1 [INFO] [stderr] Checking multimap v0.8.3 [INFO] [stderr] Checking statrs v0.13.0 [INFO] [stderr] Checking csv v1.1.6 [INFO] [stderr] Checking gfa v0.10.0 [INFO] [stderr] Checking handlegraph v0.7.0-alpha.7 (https://github.com/chfi/rs-handlegraph#5d44c62c) [INFO] [stderr] Checking variation_graph v0.1.0 (/opt/rustwide/workdir) [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] 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] 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] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 71 | use crate::multiple_alignment_format::MAFBlock; [INFO] [stdout] | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [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] help: consider importing this enum instead [INFO] [stdout] | [INFO] [stdout] 72 | use crate::multiple_alignment_format::MAFBlockEntry; [INFO] [stdout] | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [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] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 73 | use crate::multiple_alignment_format::MAFBlockAlignedEntry; [INFO] [stdout] | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [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] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 74 | use crate::multiple_alignment_format::MAFBlockUnalignedEntry; [INFO] [stdout] | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [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] help: consider importing this enum instead [INFO] [stdout] | [INFO] [stdout] 75 | use crate::multiple_alignment_format::Strand; [INFO] [stdout] | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [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] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 76 | use crate::multiple_alignment_format::AlignedContext; [INFO] [stdout] | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [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] help: consider importing this enum instead [INFO] [stdout] | [INFO] [stdout] 77 | use crate::multiple_alignment_format::AlignedContextStatus; [INFO] [stdout] | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [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] help: consider importing this enum instead [INFO] [stdout] | [INFO] [stdout] 78 | use crate::multiple_alignment_format::UnalignedContextStatus; [INFO] [stdout] | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [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] warning: field `last_node` is never read [INFO] [stdout] --> src/variation_graph.rs:32:5 [INFO] [stdout] | [INFO] [stdout] 29 | pub struct VariationGraph { [INFO] [stdout] | -------------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 32 | last_node : Handle, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `VariationGraph` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 3 warnings emitted [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] [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] [stderr] error: could not compile `variation_graph` (lib test) 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] running `Command { std: "docker" "inspect" "76cbaa372c3b8b92383e0823285e20a942caba40ceb209be33bf6965a6e123d4", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "76cbaa372c3b8b92383e0823285e20a942caba40ceb209be33bf6965a6e123d4", kill_on_drop: false }` [INFO] [stdout] 76cbaa372c3b8b92383e0823285e20a942caba40ceb209be33bf6965a6e123d4