[INFO] cloning repository https://github.com/kgori/alignomatic
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/kgori/alignomatic" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Falignomatic", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Falignomatic'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 88416e910ebe416a73bd4e9ff82db3ecd875f0b1
[INFO] checking kgori/alignomatic against c397dae808f70caebab1fc4e11b3edf7e59f58c7 for pr-158759-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Falignomatic" "/workspace/builds/worker-4-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-4-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/kgori/alignomatic
[INFO] finished tweaking git repo https://github.com/kgori/alignomatic
[INFO] tweaked toml for git repo https://github.com/kgori/alignomatic written to /workspace/builds/worker-4-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/kgori/alignomatic on toolchain c397dae808f70caebab1fc4e11b3edf7e59f58c7
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+c397dae808f70caebab1fc4e11b3edf7e59f58c7" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/kgori/alignomatic 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" "+c397dae808f70caebab1fc4e11b3edf7e59f58c7" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Updating git repository `https://github.com/kgori/rust-bwa.git`
[INFO] [stderr]     Updating git submodule `https://github.com/10XGenomics/bwa.git`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded zmij v1.0.19
[INFO] [stderr]   Downloaded rustc_version v0.1.7
[INFO] [stderr]   Downloaded rust-htslib v1.0.0
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded semver v0.1.20
[INFO] [stderr]   Downloaded env_filter v0.1.4
[INFO] [stderr]   Downloaded clap_lex v0.7.7
[INFO] [stderr]   Downloaded derive-new v0.6.0
[INFO] [stderr]   Downloaded enum-map-derive v0.17.0
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded derive-new v0.7.0
[INFO] [stderr]   Downloaded custom_derive v0.1.7
[INFO] [stderr]   Downloaded derefable v0.1.0
[INFO] [stderr]   Downloaded bgzf v0.2.0
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded linear-map v1.2.0
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded bgzip v0.3.1
[INFO] [stderr]   Downloaded enum-map v2.7.3
[INFO] [stderr]   Downloaded rand_distr v0.4.3
[INFO] [stderr]   Downloaded ieee754 v0.2.6
[INFO] [stderr]   Downloaded liblzma v0.3.6
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded portable-atomic-util v0.2.5
[INFO] [stderr]   Downloaded clap v4.5.57
[INFO] [stderr]   Downloaded simba v0.9.1
[INFO] [stderr]   Downloaded jiff-static v0.2.18
[INFO] [stderr]   Downloaded zerocopy-derive v0.8.38
[INFO] [stderr]   Downloaded clap_builder v4.5.57
[INFO] [stderr]   Downloaded statrs v0.18.0
[INFO] [stderr]   Downloaded libdeflate-sys v0.7.5
[INFO] [stderr]   Downloaded bindgen v0.69.5
[INFO] [stderr]   Downloaded bio v3.0.0
[INFO] [stderr]   Downloaded ndarray v0.16.1
[INFO] [stderr]   Downloaded zerocopy v0.8.38
[INFO] [stderr]   Downloaded jiff v0.2.18
[INFO] [stderr]   Downloaded libz-sys v1.1.23
[INFO] [stderr]   Downloaded liblzma-sys v0.3.13
[INFO] [stderr]   Downloaded hts-sys v2.2.0
[INFO] [stderr]   Downloaded libdeflater v0.7.5
[INFO] [stderr]   Downloaded niffler v2.7.0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,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" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:3d5ced03c013a94a2f102a4510f48a6e9184255caf5fd8244f58017bde7f5210" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 1442ad07e57287af71e1c22badf4b8152bb07cce93946f6e72b74cc8833a680c
[INFO] running `Command { std: "docker" "start" "1442ad07e57287af71e1c22badf4b8152bb07cce93946f6e72b74cc8833a680c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "1442ad07e57287af71e1c22badf4b8152bb07cce93946f6e72b74cc8833a680c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "1442ad07e57287af71e1c22badf4b8152bb07cce93946f6e72b74cc8833a680c" "/opt/rustwide/cargo-home/bin/cargo" "+c397dae808f70caebab1fc4e11b3edf7e59f58c7" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "1442ad07e57287af71e1c22badf4b8152bb07cce93946f6e72b74cc8833a680c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "1442ad07e57287af71e1c22badf4b8152bb07cce93946f6e72b74cc8833a680c" "/opt/rustwide/cargo-home/bin/cargo" "+c397dae808f70caebab1fc4e11b3edf7e59f58c7" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.180
[INFO] [stderr]    Compiling unicode-ident v1.0.22
[INFO] [stderr]    Compiling quote v1.0.44
[INFO] [stderr]    Compiling serde_core v1.0.228
[INFO] [stderr]     Checking memchr v2.7.6
[INFO] [stderr]    Compiling zerocopy v0.8.38
[INFO] [stderr]    Compiling glob v0.3.3
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]     Checking writeable v0.6.2
[INFO] [stderr]     Checking litemap v0.8.1
[INFO] [stderr]    Compiling regex-syntax v0.8.9
[INFO] [stderr]    Compiling minimal-lexical v0.2.1
[INFO] [stderr]    Compiling icu_properties_data v2.1.2
[INFO] [stderr]    Compiling icu_normalizer_data v2.1.1
[INFO] [stderr]    Compiling proc-macro2 v1.0.106
[INFO] [stderr]    Compiling libloading v0.8.9
[INFO] [stderr]    Compiling matrixmultiply v0.3.10
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling proc-macro2 v0.4.30
[INFO] [stderr]    Compiling either v1.15.0
[INFO] [stderr]    Compiling bindgen v0.69.5
[INFO] [stderr]    Compiling clang-sys v1.8.1
[INFO] [stderr]     Checking bytemuck v1.25.0
[INFO] [stderr]     Checking safe_arch v0.7.4
[INFO] [stderr]    Compiling itertools v0.12.1
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling unicode-xid v0.1.0
[INFO] [stderr]     Checking aho-corasick v1.1.4
[INFO] [stderr]     Checking smallvec v1.15.1
[INFO] [stderr]    Compiling lazy_static v1.5.0
[INFO] [stderr]    Compiling bitflags v2.10.0
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]    Compiling lazycell v1.3.0
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling rustc-hash v1.1.0
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking wide v0.7.33
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]    Compiling nom v7.1.3
[INFO] [stderr]    Compiling syn v2.0.114
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling syn v0.15.44
[INFO] [stderr]     Checking anstyle-parse v0.2.7
[INFO] [stderr]    Compiling proc-macro-error-attr2 v2.0.0
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]     Checking foldhash v0.1.5
[INFO] [stderr]     Checking anstyle-query v1.1.5
[INFO] [stderr]     Checking simd-adler32 v0.3.8
[INFO] [stderr]    Compiling anyhow v1.0.100
[INFO] [stderr]    Compiling quote v0.6.13
[INFO] [stderr]     Checking is_terminal_polyfill v1.70.2
[INFO] [stderr]     Checking hashbrown v0.16.1
[INFO] [stderr]     Checking anstyle v1.0.13
[INFO] [stderr]     Checking itoa v1.0.17
[INFO] [stderr]     Checking percent-encoding v2.3.2
[INFO] [stderr]    Compiling zstd-safe v7.2.4
[INFO] [stderr]     Checking getrandom v0.2.17
[INFO] [stderr]     Checking colorchoice v1.0.4
[INFO] [stderr]    Compiling jobserver v0.1.34
[INFO] [stderr]     Checking anstream v0.6.21
[INFO] [stderr]     Checking miniz_oxide v0.8.9
[INFO] [stderr]     Checking form_urlencoded v1.2.2
[INFO] [stderr]    Compiling cc v1.2.55
[INFO] [stderr]     Checking hashbrown v0.15.5
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking csv-core v0.1.13
[INFO] [stderr]    Compiling regex-automata v0.4.14
[INFO] [stderr]     Checking bit-vec v0.8.0
[INFO] [stderr]     Checking ryu v1.0.22
[INFO] [stderr]     Checking fixedbitset v0.5.7
[INFO] [stderr]     Checking indexmap v2.13.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]    Compiling rustix v1.1.3
[INFO] [stderr]    Compiling zmij v1.0.19
[INFO] [stderr]     Checking flate2 v1.1.9
[INFO] [stderr]    Compiling cexpr v0.6.0
[INFO] [stderr]     Checking bit-set v0.8.0
[INFO] [stderr]     Checking itertools v0.14.0
[INFO] [stderr]     Checking ndarray v0.16.1
[INFO] [stderr]     Checking ordered-float v5.1.0
[INFO] [stderr]     Checking simba v0.9.1
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking clap_lex v0.7.7
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]    Compiling cmake v0.1.57
[INFO] [stderr]     Checking csv v1.4.0
[INFO] [stderr]     Checking petgraph v0.8.3
[INFO] [stderr]     Checking serde_bytes v0.11.19
[INFO] [stderr]     Checking strum v0.26.3
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking linux-raw-sys v0.11.0
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking regex v1.12.3
[INFO] [stderr]     Checking bytecount v0.6.9
[INFO] [stderr]     Checking strsim v0.11.1
[INFO] [stderr]     Checking getrandom v0.3.4
[INFO] [stderr]     Checking clap_builder v4.5.57
[INFO] [stderr]    Compiling libz-sys v1.1.23
[INFO] [stderr]    Compiling zstd-sys v2.0.16+zstd.1.5.7
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling libdeflate-sys v0.7.5
[INFO] [stderr]    Compiling liblzma-sys v0.3.13
[INFO] [stderr]    Compiling bwa-sys v0.1.0 (https://github.com/kgori/rust-bwa.git?tag=v0.1.5#de5e6235)
[INFO] [stderr]    Compiling derefable v0.1.0
[INFO] [stderr]     Checking ppv-lite86 v0.2.21
[INFO] [stderr]    Compiling blake3 v1.8.3
[INFO] [stderr]     Checking env_filter v0.1.4
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking jiff v0.2.18
[INFO] [stderr]     Checking fastrand v2.3.0
[INFO] [stderr]     Checking bzip2 v0.4.4
[INFO] [stderr]     Checking once_cell v1.21.3
[INFO] [stderr]    Compiling synstructure v0.13.2
[INFO] [stderr]    Compiling proc-macro-error2 v2.0.1
[INFO] [stderr]     Checking constant_time_eq v0.4.2
[INFO] [stderr]     Checking tempfile v3.24.0
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking serde_json v1.0.149
[INFO] [stderr]     Checking num_cpus v1.17.0
[INFO] [stderr]    Compiling zerofrom-derive v0.1.6
[INFO] [stderr]    Compiling yoke-derive v0.8.1
[INFO] [stderr]    Compiling zerovec-derive v0.11.2
[INFO] [stderr]    Compiling displaydoc v0.2.5
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling thiserror-impl v2.0.18
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]     Checking nalgebra v0.33.2
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]     Checking zerofrom v0.1.6
[INFO] [stderr]    Compiling derive-new v0.7.0
[INFO] [stderr]    Compiling getset v0.1.6
[INFO] [stderr]     Checking yoke v0.8.1
[INFO] [stderr]     Checking thiserror v1.0.69
[INFO] [stderr]     Checking libdeflater v0.7.5
[INFO] [stderr]     Checking bgzip v0.3.1
[INFO] [stderr]    Compiling clap_derive v4.5.55
[INFO] [stderr]     Checking thiserror v2.0.18
[INFO] [stderr]     Checking zerovec v0.11.5
[INFO] [stderr]     Checking zerotrie v0.2.3
[INFO] [stderr]     Checking bgzf v0.2.0
[INFO] [stderr]     Checking tinystr v0.8.2
[INFO] [stderr]     Checking potential_utf v0.1.4
[INFO] [stderr]     Checking icu_collections v2.1.1
[INFO] [stderr]     Checking icu_locale_core v2.1.1
[INFO] [stderr]     Checking liblzma v0.3.6
[INFO] [stderr]     Checking serde v1.0.228
[INFO] [stderr]     Checking icu_provider v2.1.1
[INFO] [stderr]     Checking env_logger v0.11.8
[INFO] [stderr]     Checking icu_normalizer v2.1.1
[INFO] [stderr]     Checking icu_properties v2.1.2
[INFO] [stderr]     Checking clap v4.5.57
[INFO] [stderr]    Compiling hts-sys v2.2.0
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking multimap v0.10.1
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking idna_adapter v1.2.1
[INFO] [stderr]     Checking zstd v0.13.3
[INFO] [stderr]     Checking idna v1.1.0
[INFO] [stderr]     Checking niffler v2.7.0
[INFO] [stderr]     Checking url v2.5.8
[INFO] [stderr]     Checking statrs v0.18.0
[INFO] [stderr]     Checking bio v3.0.0
[INFO] [stderr]     Checking rust-htslib v1.0.0
[INFO] [stderr]     Checking bwa v0.1.5 (https://github.com/kgori/rust-bwa.git?tag=v0.1.5#de5e6235)
[INFO] [stderr]     Checking alignomatic v0.6.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 56.77s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: proc-macro-error2 v2.0.1
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] running `Command { std: "docker" "inspect" "1442ad07e57287af71e1c22badf4b8152bb07cce93946f6e72b74cc8833a680c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "1442ad07e57287af71e1c22badf4b8152bb07cce93946f6e72b74cc8833a680c", kill_on_drop: false }`
[INFO] [stdout] 1442ad07e57287af71e1c22badf4b8152bb07cce93946f6e72b74cc8833a680c
