[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 against try#a7a572ce3edd6d476191fbfe92c9c1986e009b34 for pr-87190-3
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FFede-Berga%2FVariation_Graph" "/workspace/builds/worker-77/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-77/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/Fede-Berga/Variation_Graph on toolchain a7a572ce3edd6d476191fbfe92c9c1986e009b34
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "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-77/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" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "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 bytemuck_derive v1.0.1
[INFO] [stderr]   Downloaded succinct v0.5.2
[INFO] [stderr]   Downloaded ordered-float v1.1.1
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[INFO] [stderr]   Downloaded bio v0.34.0
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-77/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-77/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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 43a665cd1516d5279cb2add8c27a2567e633016f6f57a9da623609a86cfb0327
[INFO] running `Command { std: "docker" "start" "-a" "43a665cd1516d5279cb2add8c27a2567e633016f6f57a9da623609a86cfb0327", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "43a665cd1516d5279cb2add8c27a2567e633016f6f57a9da623609a86cfb0327", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "43a665cd1516d5279cb2add8c27a2567e633016f6f57a9da623609a86cfb0327", kill_on_drop: false }`
[INFO] [stdout] 43a665cd1516d5279cb2add8c27a2567e633016f6f57a9da623609a86cfb0327
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-77/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-77/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" "ghcr.io/rust-lang/crates-build-env/linux@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 12414fb72f8e77660404404622d0ac8fee88098c29f8804498c7dfa19a28384b
[INFO] running `Command { std: "docker" "start" "-a" "12414fb72f8e77660404404622d0ac8fee88098c29f8804498c7dfa19a28384b", kill_on_drop: false }`
[INFO] [stderr] Copying to /tmp/fixit
[INFO] [stderr] Running `cargo fix --edition`
[INFO] [stderr]    Compiling proc-macro2 v1.0.27
[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
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[INFO] [stderr]    Compiling crossbeam-epoch v0.9.5
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[INFO] [stderr]    Compiling rayon-core v1.9.1
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[INFO] [stderr]    Compiling anyhow v1.0.40
[INFO] [stderr]     Checking regex-syntax v0.6.25
[INFO] [stderr]     Checking regex-automata v0.1.10
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling lexical-core v0.7.6
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]    Compiling unicode-segmentation v1.7.1
[INFO] [stderr]     Checking arrayvec v0.5.2
[INFO] [stderr]     Checking hashbrown v0.9.1
[INFO] [stderr]    Compiling ndarray v0.14.0
[INFO] [stderr]     Checking rand_core v0.6.2
[INFO] [stderr]     Checking fixedbitset v0.2.0
[INFO] [stderr]     Checking array-macro v1.0.5
[INFO] [stderr]    Compiling bio v0.34.0
[INFO] [stderr]     Checking bit-vec v0.6.3
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[INFO] [stderr]     Checking triple_accel v0.3.4
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking strum v0.20.0
[INFO] [stderr]     Checking maplit v1.0.2
[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 num-complex v0.2.4
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[INFO] [stderr]    Compiling rayon v1.5.1
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[INFO] [stderr]    Compiling rustc_version v0.1.7
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[INFO] [stderr]     Checking wyhash v0.5.0
[INFO] [stderr]    Compiling heck v0.3.3
[INFO] [stderr]     Checking bit-set v0.5.2
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[INFO] [stderr]    Compiling newtype_derive v0.1.6
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[INFO] [stderr]     Checking memmap v0.7.0
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[INFO] [stderr]     Checking rand v0.7.3
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[INFO] [stderr]     Checking rand_distr v0.2.2
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[INFO] [stderr]     Checking num-complex v0.3.1
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking succinct v0.5.2
[INFO] [stderr]     Checking ordered-float v1.1.1
[INFO] [stderr]     Checking alga v0.9.3
[INFO] [stderr]     Checking nalgebra v0.19.0
[INFO] [stderr]     Checking boomphf v0.5.9
[INFO] [stderr]    Compiling bytemuck_derive v1.0.1
[INFO] [stderr]    Compiling thiserror-impl v1.0.25
[INFO] [stderr]    Compiling strum_macros v0.20.1
[INFO] [stderr]    Compiling enum-map-derive v0.4.6
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling getset v0.0.9
[INFO] [stderr]     Checking enum-map v0.6.4
[INFO] [stderr]     Checking bytemuck v1.5.1
[INFO] [stderr]     Checking thiserror v1.0.25
[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 multimap v0.8.3
[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 statrs v0.13.0
[INFO] [stderr]     Checking variation_graph v0.1.0 (/tmp/fixit)
[INFO] [stderr]    Migrating src/lib.rs from 2018 edition to 2021
[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] [stderr]        Fixed src/multiple_alignment_format/mod.rs (1 fix)
[INFO] [stderr]        Fixed src/alignment_parser.rs (1 fix)
[INFO] [stderr] error: build failed
[INFO] [stderr] error: failed to migrate to next edition
[INFO] [stderr] 
[INFO] [stderr] Caused by:
[INFO] [stderr]   process didn't exit successfully: `cargo fix --edition --allow-no-vcs --allow-dirty --frozen --all --all-targets --message-format=json` (exit status: 101)
[INFO] running `Command { std: "docker" "inspect" "12414fb72f8e77660404404622d0ac8fee88098c29f8804498c7dfa19a28384b", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "12414fb72f8e77660404404622d0ac8fee88098c29f8804498c7dfa19a28384b", kill_on_drop: false }`
[INFO] [stdout] 12414fb72f8e77660404404622d0ac8fee88098c29f8804498c7dfa19a28384b