[INFO] cloning repository https://github.com/AI4S-YB/Rustpair
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/AI4S-YB/Rustpair" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FAI4S-YB%2FRustpair", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FAI4S-YB%2FRustpair'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] cd2682a22e963a34d60cf68aff52bab9e9a80c8c
[INFO] checking AI4S-YB/Rustpair against 79c0559184f27f4433a6fbc260b950d06d4a4889 for pr-162233-crater-rollup
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FAI4S-YB%2FRustpair" "/workspace/builds/worker-2-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/AI4S-YB/Rustpair
[INFO] finished tweaking git repo https://github.com/AI4S-YB/Rustpair
[INFO] tweaked toml for git repo https://github.com/AI4S-YB/Rustpair written to /workspace/builds/worker-2-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/AI4S-YB/Rustpair on toolchain 79c0559184f27f4433a6fbc260b950d06d4a4889
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+79c0559184f27f4433a6fbc260b950d06d4a4889" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/AI4S-YB/Rustpair 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" "+79c0559184f27f4433a6fbc260b950d06d4a4889" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/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@sha256:8683fc1fc2eb5c9ac98e0d076ab094b2ffac7f99da555d2b6a2e27f346de2ec7" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 0eca3ffd74c92914d49bc27941c997b794440b276b09458b319c749670dee9c9
[INFO] running `Command { std: "docker" "start" "0eca3ffd74c92914d49bc27941c997b794440b276b09458b319c749670dee9c9", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "0eca3ffd74c92914d49bc27941c997b794440b276b09458b319c749670dee9c9", 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" "0eca3ffd74c92914d49bc27941c997b794440b276b09458b319c749670dee9c9" "/opt/rustwide/cargo-home/bin/cargo" "+79c0559184f27f4433a6fbc260b950d06d4a4889" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "0eca3ffd74c92914d49bc27941c997b794440b276b09458b319c749670dee9c9", 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" "0eca3ffd74c92914d49bc27941c997b794440b276b09458b319c749670dee9c9" "/opt/rustwide/cargo-home/bin/cargo" "+79c0559184f27f4433a6fbc260b950d06d4a4889" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.185
[INFO] [stderr]     Checking aho-corasick v1.1.4
[INFO] [stderr]     Checking regex-syntax v0.8.10
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling displaydoc v0.2.5
[INFO] [stderr]     Checking zerofrom v0.1.7
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]     Checking smallvec v1.15.1
[INFO] [stderr]    Compiling serde_core v1.0.228
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]     Checking yoke v0.8.2
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking zerovec v0.11.6
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling glob v0.3.3
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking zerotrie v0.2.4
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling matrixmultiply v0.3.10
[INFO] [stderr]     Checking tinystr v0.8.3
[INFO] [stderr]     Checking potential_utf v0.1.5
[INFO] [stderr]     Checking icu_collections v2.2.0
[INFO] [stderr]     Checking icu_locale_core v2.2.0
[INFO] [stderr]     Checking percent-encoding v2.3.2
[INFO] [stderr]    Compiling getrandom v0.4.2
[INFO] [stderr]     Checking form_urlencoded v1.2.2
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling jobserver v0.1.34
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling cc v1.2.60
[INFO] [stderr]     Checking icu_provider v2.2.0
[INFO] [stderr]     Checking regex-automata v0.4.14
[INFO] [stderr]     Checking thiserror v1.0.69
[INFO] [stderr]     Checking bitflags v2.11.1
[INFO] [stderr]     Checking icu_normalizer v2.2.0
[INFO] [stderr]     Checking icu_properties v2.2.0
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]     Checking simd-adler32 v0.3.9
[INFO] [stderr]     Checking log v0.4.29
[INFO] [stderr]     Checking hashbrown v0.17.0
[INFO] [stderr]    Compiling cmake v0.1.58
[INFO] [stderr]    Compiling openssl-src v300.6.0+3.6.2
[INFO] [stderr]     Checking miniz_oxide v0.8.9
[INFO] [stderr]     Checking idna_adapter v1.2.1
[INFO] [stderr]     Checking rustix v1.1.4
[INFO] [stderr]     Checking indexmap v2.14.0
[INFO] [stderr]     Checking idna v1.1.0
[INFO] [stderr]    Compiling libz-sys v1.1.28
[INFO] [stderr]    Compiling openssl-sys v0.9.113
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling curl-sys v0.4.87+curl-8.19.0
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]     Checking regex v1.12.3
[INFO] [stderr]    Compiling hts-sys v2.2.0
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]     Checking url v2.5.8
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking env_filter v1.0.1
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]    Compiling thiserror-impl v2.0.18
[INFO] [stderr]     Checking csv-core v0.1.13
[INFO] [stderr]     Checking twox-hash v2.1.2
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking jiff v0.2.23
[INFO] [stderr]     Checking unsafe-libyaml v0.2.11
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking ndarray v0.16.1
[INFO] [stderr]     Checking tempfile v3.27.0
[INFO] [stderr]     Checking serde v1.0.228
[INFO] [stderr]     Checking csv v1.4.0
[INFO] [stderr]     Checking lz4_flex v0.11.6
[INFO] [stderr]     Checking flate2 v1.1.9
[INFO] [stderr]     Checking rayon v1.12.0
[INFO] [stderr]     Checking serde_yaml v0.9.34+deprecated
[INFO] [stderr]     Checking thiserror v2.0.18
[INFO] [stderr]     Checking itertools v0.13.0
[INFO] [stderr]     Checking memmap2 v0.9.10
[INFO] [stderr]     Checking kdtree v0.2.1
[INFO] [stderr]     Checking env_logger v0.11.10
[INFO] [stderr]     Checking rust-htslib v0.46.0
[INFO] [stderr]     Checking pairtools v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr] warning: unused dependency `csv`
[INFO] [stderr]  --> Cargo.toml:7:1
[INFO] [stderr]   |
[INFO] [stderr] 7 | csv = "1.3"
[INFO] [stderr]   | ^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `cargo::unused_dependencies` is set to `warn` by default
[INFO] [stderr] help: consider removing the dependency on `csv`
[INFO] [stderr] warning: unused dependency `itertools`
[INFO] [stderr]   --> Cargo.toml:10:1
[INFO] [stderr]    |
[INFO] [stderr] 10 | itertools = "0.13"
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `itertools`
[INFO] [stderr] warning: unused dependency `kdtree`
[INFO] [stderr]   --> Cargo.toml:11:1
[INFO] [stderr]    |
[INFO] [stderr] 11 | kdtree = "0.2"
[INFO] [stderr]    | ^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `kdtree`
[INFO] [stderr] warning: unused dependency `lz4_flex`
[INFO] [stderr]   --> Cargo.toml:13:1
[INFO] [stderr]    |
[INFO] [stderr] 13 | lz4_flex = "0.11"
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `lz4_flex`
[INFO] [stderr] warning: unused dependency `memmap2`
[INFO] [stderr]   --> Cargo.toml:14:1
[INFO] [stderr]    |
[INFO] [stderr] 14 | memmap2 = "0.9"
[INFO] [stderr]    | ^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `memmap2`
[INFO] [stderr] warning: unused dependency `ndarray`
[INFO] [stderr]   --> Cargo.toml:15:1
[INFO] [stderr]    |
[INFO] [stderr] 15 | ndarray = "0.16"
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `ndarray`
[INFO] [stderr] warning: unused dependency `serde_yaml`
[INFO] [stderr]   --> Cargo.toml:18:1
[INFO] [stderr]    |
[INFO] [stderr] 18 | serde_yaml = "0.9"
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `serde_yaml`
[INFO] [stderr] warning: unused dependency `tempfile`
[INFO] [stderr]   --> Cargo.toml:19:1
[INFO] [stderr]    |
[INFO] [stderr] 19 | tempfile = "3"
[INFO] [stderr]    | ^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `tempfile`
[INFO] [stderr] warning: unused dependency `thiserror`
[INFO] [stderr]   --> Cargo.toml:20:1
[INFO] [stderr]    |
[INFO] [stderr] 20 | thiserror = "2"
[INFO] [stderr]    | ^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `thiserror`
[INFO] [stderr] warning: `pairtools` (manifest) generated 9 warnings
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 6m 34s
[INFO] running `Command { std: "docker" "inspect" "0eca3ffd74c92914d49bc27941c997b794440b276b09458b319c749670dee9c9", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "0eca3ffd74c92914d49bc27941c997b794440b276b09458b319c749670dee9c9", kill_on_drop: false }`
[INFO] [stdout] 0eca3ffd74c92914d49bc27941c997b794440b276b09458b319c749670dee9c9
