[INFO] cloning repository https://github.com/tomdstanton/pyggcat
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/tomdstanton/pyggcat" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Ftomdstanton%2Fpyggcat", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Ftomdstanton%2Fpyggcat'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 59c5a2a13afd6a60a2b53345457bab4127faba65
[INFO] checking tomdstanton/pyggcat against master#31a9463c6e2794a59ce57a8f37abc6966afc2a58 for pr-149045
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Ftomdstanton%2Fpyggcat" "/workspace/builds/worker-7-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/tomdstanton/pyggcat
[INFO] finished tweaking git repo https://github.com/tomdstanton/pyggcat
[INFO] tweaked toml for git repo https://github.com/tomdstanton/pyggcat written to /workspace/builds/worker-7-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/tomdstanton/pyggcat on toolchain 31a9463c6e2794a59ce57a8f37abc6966afc2a58
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+31a9463c6e2794a59ce57a8f37abc6966afc2a58" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/tomdstanton/pyggcat 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" "+31a9463c6e2794a59ce57a8f37abc6966afc2a58" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating git repository `https://github.com/algbio/ggcat.git`
[INFO] [stderr]     Updating git submodule `https://github.com/Guilucand/dynamic-dispatch-rs.git`
[INFO] [stderr]     Updating git submodule `https://github.com/Guilucand/instrumenter-rs.git`
[INFO] [stderr]     Updating git submodule `https://github.com/Guilucand/mt-debug-counters-rs.git`
[INFO] [stderr]     Updating git submodule `https://github.com/Guilucand/nightly-quirks-rs.git`
[INFO] [stderr]     Updating git submodule `https://github.com/Guilucand/papi-bindings-rs.git`
[INFO] [stderr]     Updating git submodule `https://github.com/Guilucand/parallel-processor-rs.git`
[INFO] [stderr]     Updating git submodule `https://github.com/Guilucand/streaming-libdeflate-rs.git`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded pyo3-macros v0.28.3
[INFO] [stderr]   Downloaded pyo3-build-config v0.28.3
[INFO] [stderr]   Downloaded target-lexicon v0.13.5
[INFO] [stderr]   Downloaded desse-derive v0.2.1
[INFO] [stderr]   Downloaded bincode_derive v2.0.1
[INFO] [stderr]   Downloaded dynamic-dispatch v0.5.4
[INFO] [stderr]   Downloaded nightly-quirks v0.1.5
[INFO] [stderr]   Downloaded mt-debug-counters v0.1.4
[INFO] [stderr]   Downloaded limits-rs v0.2.0
[INFO] [stderr]   Downloaded desse v0.2.1
[INFO] [stderr]   Downloaded traitgraph v8.1.2
[INFO] [stderr]   Downloaded pyo3-macros-backend v0.28.3
[INFO] [stderr]   Downloaded filebuffer v1.0.1
[INFO] [stderr]   Downloaded traitsequence v8.1.2
[INFO] [stderr]   Downloaded permutation v0.4.1
[INFO] [stderr]   Downloaded instrumenter-proc-macro v0.1.1
[INFO] [stderr]   Downloaded disjoint-sets v0.4.2
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded memory-stats v1.2.0
[INFO] [stderr]   Downloaded traitgraph-algo v8.1.2
[INFO] [stderr]   Downloaded streaming-libdeflate-rs v0.2.3
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded instrumenter v0.1.4
[INFO] [stderr]   Downloaded bitvector v0.1.5
[INFO] [stderr]   Downloaded virtue v0.0.18
[INFO] [stderr]   Downloaded atomic-counter v1.0.1
[INFO] [stderr]   Downloaded matchtigs v2.1.9
[INFO] [stderr]   Downloaded genome-graph v11.0.0
[INFO] [stderr]   Downloaded compact-genome v12.5.0
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded custom_derive v0.1.7
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded parallel-processor v0.2.3
[INFO] [stderr]   Downloaded bigraph v5.0.1
[INFO] [stderr]   Downloaded binary-heap-plus v0.5.0
[INFO] [stderr]   Downloaded compare v0.1.0
[INFO] [stderr]   Downloaded pyo3-ffi v0.28.3
[INFO] [stderr]   Downloaded procfs v0.18.0
[INFO] [stderr]   Downloaded procfs-core v0.18.0
[INFO] [stderr]   Downloaded bio v2.3.0
[INFO] [stderr]   Downloaded dynamic-dispatch-proc-macro v0.5.0
[INFO] [stderr]   Downloaded bitbound v0.1.1
[INFO] [stderr]   Downloaded pyo3 v0.28.3
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+31a9463c6e2794a59ce57a8f37abc6966afc2a58" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 077d83d149bfa020e5e00aebe3ed7279996075f0c57efd8ffdfa50cc915b74e9
[INFO] running `Command { std: "docker" "start" "-a" "077d83d149bfa020e5e00aebe3ed7279996075f0c57efd8ffdfa50cc915b74e9", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "077d83d149bfa020e5e00aebe3ed7279996075f0c57efd8ffdfa50cc915b74e9", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "077d83d149bfa020e5e00aebe3ed7279996075f0c57efd8ffdfa50cc915b74e9", kill_on_drop: false }`
[INFO] [stdout] 077d83d149bfa020e5e00aebe3ed7279996075f0c57efd8ffdfa50cc915b74e9
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+31a9463c6e2794a59ce57a8f37abc6966afc2a58" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] c1f3541fc50c178a79233d666a26643365975360065699359f7240a2e3925a06
[INFO] running `Command { std: "docker" "start" "-a" "c1f3541fc50c178a79233d666a26643365975360065699359f7240a2e3925a06", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.185
[INFO] [stderr]     Checking lock_api v0.4.14
[INFO] [stderr]    Compiling proc-macro2 v0.4.30
[INFO] [stderr]    Compiling unicode-xid v0.1.0
[INFO] [stderr]    Compiling syn v2.0.117
[INFO] [stderr]     Checking itertools v0.14.0
[INFO] [stderr]    Compiling cc v1.2.60
[INFO] [stderr]    Compiling syn v0.15.44
[INFO] [stderr]    Compiling rayon-core v1.13.0
[INFO] [stderr]    Compiling object v0.37.3
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]     Checking bitflags v2.11.1
[INFO] [stderr]    Compiling rustix v1.1.4
[INFO] [stderr]     Checking regex-automata v0.4.14
[INFO] [stderr]     Checking chrono v0.4.44
[INFO] [stderr]     Checking crossbeam-channel v0.5.15
[INFO] [stderr]     Checking crossbeam-queue v0.3.12
[INFO] [stderr]     Checking linux-raw-sys v0.12.1
[INFO] [stderr]    Compiling memchr v2.8.0
[INFO] [stderr]    Compiling procfs v0.18.0
[INFO] [stderr]     Checking gimli v0.32.3
[INFO] [stderr]    Compiling virtue v0.0.18
[INFO] [stderr]     Checking typenum v1.20.0
[INFO] [stderr]     Checking crossbeam v0.8.4
[INFO] [stderr]     Checking json v0.12.4
[INFO] [stderr]    Compiling quote v0.6.13
[INFO] [stderr]     Checking bytesize v1.3.3
[INFO] [stderr]    Compiling aho-corasick v1.1.4
[INFO] [stderr]     Checking unty v0.0.4
[INFO] [stderr]    Compiling regex-syntax v0.8.10
[INFO] [stderr]     Checking rustc-demangle v0.1.27
[INFO] [stderr]    Compiling bincode_derive v2.0.1
[INFO] [stderr]     Checking getrandom v0.3.4
[INFO] [stderr]     Checking getrandom v0.2.17
[INFO] [stderr]     Checking parking_lot_core v0.9.12
[INFO] [stderr]     Checking rand_core v0.9.5
[INFO] [stderr]     Checking ahash v0.8.12
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking parking_lot v0.12.5
[INFO] [stderr]     Checking rand_chacha v0.9.0
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking hashbrown v0.14.5
[INFO] [stderr]     Checking nightly-quirks v0.1.5
[INFO] [stderr]     Checking rand v0.9.4
[INFO] [stderr]     Checking rand v0.8.6
[INFO] [stderr]    Compiling lz4-sys v1.11.1+lz4-1.10.0
[INFO] [stderr]     Checking procfs-core v0.18.0
[INFO] [stderr]     Checking filebuffer v1.0.1
[INFO] [stderr]     Checking bincode v2.0.1
[INFO] [stderr]     Checking mt-debug-counters v0.1.4
[INFO] [stderr]     Checking page_size v0.6.0
[INFO] [stderr]     Checking addr2line v0.25.1
[INFO] [stderr]     Checking rayon v1.12.0
[INFO] [stderr]     Checking arc-swap v1.9.1
[INFO] [stderr]     Checking rustc-hash v2.1.2
[INFO] [stderr]     Checking dashmap v6.1.0
[INFO] [stderr]     Checking replace_with v0.1.8
[INFO] [stderr]     Checking unchecked-index v0.2.2
[INFO] [stderr]    Compiling heck v0.3.3
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]    Compiling target-lexicon v0.13.5
[INFO] [stderr]     Checking serde_json v1.0.149
[INFO] [stderr]     Checking bitbound v0.1.1
[INFO] [stderr]     Checking bstr v1.12.1
[INFO] [stderr]     Checking hashbrown v0.17.0
[INFO] [stderr]     Checking roaring v0.10.12
[INFO] [stderr]     Checking atoi v2.0.0
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling desse-derive v0.2.1
[INFO] [stderr]     Checking bitvec v1.0.1
[INFO] [stderr]     Checking csv-core v0.1.13
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling pyo3-build-config v0.28.3
[INFO] [stderr]     Checking indexmap v2.14.0
[INFO] [stderr]     Checking traitsequence v8.1.2
[INFO] [stderr]     Checking desse v0.2.1
[INFO] [stderr]     Checking csv v1.4.0
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking tokio v1.52.1
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]    Compiling ref-cast v1.0.25
[INFO] [stderr]     Checking regex v1.12.3
[INFO] [stderr]     Checking bit-vec v0.8.0
[INFO] [stderr]     Checking backtrace v0.3.76
[INFO] [stderr]    Compiling time-core v0.1.8
[INFO] [stderr]    Compiling num-conv v0.2.1
[INFO] [stderr]     Checking nalgebra v0.33.3
[INFO] [stderr]    Compiling instrumenter-proc-macro v0.1.1
[INFO] [stderr]     Checking bit-set v0.8.0
[INFO] [stderr]     Checking ndarray v0.16.1
[INFO] [stderr]     Checking instrumenter v0.1.4
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v5.3.0
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]    Compiling time-macros v0.2.27
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking bitvector v0.1.5
[INFO] [stderr]     Checking petgraph v0.7.1
[INFO] [stderr]     Checking petgraph v0.8.3
[INFO] [stderr]     Checking strum v0.26.3
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking clap_builder v4.6.0
[INFO] [stderr]     Checking disjoint-sets v0.4.2
[INFO] [stderr]     Checking memory-stats v1.2.0
[INFO] [stderr]     Checking permutation v0.4.1
[INFO] [stderr]     Checking atomic-counter v1.0.1
[INFO] [stderr]     Checking compare v0.1.0
[INFO] [stderr]     Checking fs_extra v1.3.0
[INFO] [stderr]     Checking binary-heap-plus v0.5.0
[INFO] [stderr]     Checking getrandom v0.4.2
[INFO] [stderr]    Compiling structopt-derive v0.4.18
[INFO] [stderr]    Compiling pyo3-ffi v0.28.3
[INFO] [stderr]    Compiling pyo3-macros-backend v0.28.3
[INFO] [stderr]    Compiling pyo3 v0.28.3
[INFO] [stderr]     Checking uuid v1.23.1
[INFO] [stderr]     Checking time v0.3.47
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling thiserror-impl v2.0.18
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling ref-cast-impl v1.0.25
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]    Compiling clap_derive v4.6.1
[INFO] [stderr]     Checking thiserror v2.0.18
[INFO] [stderr]     Checking simplelog v0.12.2
[INFO] [stderr]     Checking compact-genome v12.5.0
[INFO] [stderr]    Compiling dynamic-dispatch-proc-macro v0.5.0
[INFO] [stderr]     Checking thiserror v1.0.69
[INFO] [stderr]     Checking traitgraph v8.1.2
[INFO] [stderr]     Checking limits-rs v0.2.0
[INFO] [stderr]     Checking fdlimit v0.3.0
[INFO] [stderr]     Checking dynamic-dispatch v0.5.4
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking traitgraph-algo v8.1.2
[INFO] [stderr]     Checking clap v4.6.1
[INFO] [stderr]     Checking bigraph v5.0.1
[INFO] [stderr]     Checking serde v1.0.228
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking ggcat-logging v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking bincode v1.3.3
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking multimap v0.10.1
[INFO] [stderr]     Checking clap v2.34.0
[INFO] [stderr]    Compiling pyo3-macros v0.28.3
[INFO] [stderr]     Checking statrs v0.18.0
[INFO] [stderr]     Checking structopt v0.3.26
[INFO] [stderr]     Checking streaming-libdeflate-rs v0.2.3
[INFO] [stderr]     Checking bio v2.3.0
[INFO] [stderr]     Checking genome-graph v11.0.0
[INFO] [stderr]     Checking matchtigs v2.1.9
[INFO] [stderr]     Checking lz4 v1.28.1
[INFO] [stderr]     Checking parallel-processor v0.2.3
[INFO] [stderr]     Checking ggcat_utils v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_config v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_hashes v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_io v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_structs v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_colors v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_minimizer_bucketing v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_assembler_pipeline v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_kmers_transform v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_assembler_minibuck v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_assembler_kmerge v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_dumper v0.1.1 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_querier v0.1.1 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat_assembler v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking ggcat-api v2.0.0 (https://github.com/algbio/ggcat.git?branch=main#2ab1d643)
[INFO] [stderr]     Checking pyggcat v0.0.1-alpha (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 52s
[INFO] running `Command { std: "docker" "inspect" "c1f3541fc50c178a79233d666a26643365975360065699359f7240a2e3925a06", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c1f3541fc50c178a79233d666a26643365975360065699359f7240a2e3925a06", kill_on_drop: false }`
[INFO] [stdout] c1f3541fc50c178a79233d666a26643365975360065699359f7240a2e3925a06