[INFO] cloning repository https://github.com/nextgenusfs/annorefine
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/nextgenusfs/annorefine" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fnextgenusfs%2Fannorefine", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fnextgenusfs%2Fannorefine'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 932b4988ba8cfcc623c88563fffb35de8943dfcd
[INFO] checking nextgenusfs/annorefine against master#ab1d2444533d829e2d5cff6634cd3c70de6d7103 for pr-147841
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fnextgenusfs%2Fannorefine" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/nextgenusfs/annorefine
[INFO] finished tweaking git repo https://github.com/nextgenusfs/annorefine
[INFO] tweaked toml for git repo https://github.com/nextgenusfs/annorefine written to /workspace/builds/worker-0-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/nextgenusfs/annorefine on toolchain ab1d2444533d829e2d5cff6634cd3c70de6d7103
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ab1d2444533d829e2d5cff6634cd3c70de6d7103" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/nextgenusfs/annorefine 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" "+ab1d2444533d829e2d5cff6634cd3c70de6d7103" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded pyo3-macros v0.22.6
[INFO] [stderr]   Downloaded unindent v0.2.4
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded ieee754 v0.2.6
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded bytecount v0.6.9
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded indoc v2.0.6
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded pyo3-build-config v0.22.6
[INFO] [stderr]   Downloaded simba v0.9.1
[INFO] [stderr]   Downloaded pyo3-macros-backend v0.22.6
[INFO] [stderr]   Downloaded pyo3-ffi v0.22.6
[INFO] [stderr]   Downloaded rust-htslib v0.50.0
[INFO] [stderr]   Downloaded statrs v0.18.0
[INFO] [stderr]   Downloaded bio v2.3.0
[INFO] [stderr]   Downloaded pyo3 v0.22.6
[INFO] [stderr]   Downloaded petgraph v0.8.2
[INFO] [stderr]   Downloaded hts-sys v2.2.0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ab1d2444533d829e2d5cff6634cd3c70de6d7103" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 3c3a25afef811f6f24808eece1c312694ef69dd05cf9d49786e85ae0db6b6787
[INFO] running `Command { std: "docker" "start" "-a" "3c3a25afef811f6f24808eece1c312694ef69dd05cf9d49786e85ae0db6b6787", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "3c3a25afef811f6f24808eece1c312694ef69dd05cf9d49786e85ae0db6b6787", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "3c3a25afef811f6f24808eece1c312694ef69dd05cf9d49786e85ae0db6b6787", kill_on_drop: false }`
[INFO] [stdout] 3c3a25afef811f6f24808eece1c312694ef69dd05cf9d49786e85ae0db6b6787
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ab1d2444533d829e2d5cff6634cd3c70de6d7103" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 5b80078c81d9776d15e4d1e2265bde52205d6fa9848b30429127b0f24d68754d
[INFO] running `Command { std: "docker" "start" "-a" "5b80078c81d9776d15e4d1e2265bde52205d6fa9848b30429127b0f24d68754d", kill_on_drop: false }`
[INFO] [stderr]    Compiling serde_core v1.0.225
[INFO] [stderr]     Checking memchr v2.7.5
[INFO] [stderr]    Compiling serde v1.0.225
[INFO] [stderr]    Compiling glob v0.3.3
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling cfg-if v1.0.3
[INFO] [stderr]    Compiling regex-syntax v0.8.6
[INFO] [stderr]    Compiling libc v0.2.175
[INFO] [stderr]    Compiling matrixmultiply v0.3.10
[INFO] [stderr]    Compiling bindgen v0.69.5
[INFO] [stderr]    Compiling either v1.15.0
[INFO] [stderr]     Checking bytemuck v1.23.2
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]    Compiling bitflags v2.9.4
[INFO] [stderr]    Compiling libloading v0.8.8
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]     Checking smallvec v1.15.1
[INFO] [stderr]    Compiling itertools v0.12.1
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking safe_arch v0.7.4
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]     Checking percent-encoding v2.3.2
[INFO] [stderr]     Checking icu_normalizer v2.0.0
[INFO] [stderr]    Compiling anyhow v1.0.99
[INFO] [stderr]     Checking indexmap v2.11.4
[INFO] [stderr]    Compiling clang-sys v1.8.1
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]    Compiling nom v7.1.3
[INFO] [stderr]     Checking idna_adapter v1.2.1
[INFO] [stderr]     Checking csv-core v0.1.12
[INFO] [stderr]     Checking idna v1.1.0
[INFO] [stderr]     Checking form_urlencoded v1.2.2
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]     Checking fixedbitset v0.5.7
[INFO] [stderr]    Compiling jobserver v0.1.34
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking wide v0.7.33
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]    Compiling cc v1.2.37
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking bit-vec v0.8.0
[INFO] [stderr]     Checking clap_builder v4.5.47
[INFO] [stderr]     Checking petgraph v0.8.2
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]     Checking bit-set v0.8.0
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]     Checking ordered-float v5.0.0
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking ndarray v0.16.1
[INFO] [stderr]    Compiling clap_derive v4.5.47
[INFO] [stderr]    Compiling derive-new v0.7.0
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking bytecount v0.6.9
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]    Compiling regex-automata v0.4.10
[INFO] [stderr]     Checking iana-time-zone v0.1.64
[INFO] [stderr]    Compiling cexpr v0.6.0
[INFO] [stderr]     Checking jiff v0.2.15
[INFO] [stderr]    Compiling cmake v0.1.54
[INFO] [stderr]    Compiling openssl-src v300.5.2+3.5.2
[INFO] [stderr]     Checking simba v0.9.1
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking strum v0.26.3
[INFO] [stderr]     Checking rayon v1.11.0
[INFO] [stderr]     Checking colored v3.0.0
[INFO] [stderr]    Compiling rustix v1.1.2
[INFO] [stderr]     Checking csv v1.3.1
[INFO] [stderr]    Compiling openssl-sys v0.9.109
[INFO] [stderr]    Compiling libz-sys v1.1.22
[INFO] [stderr]    Compiling curl-sys v0.4.83+curl-8.15.0
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking multimap v0.10.1
[INFO] [stderr]     Checking url v2.5.7
[INFO] [stderr]     Checking chrono v0.4.42
[INFO] [stderr]     Checking clap v4.5.47
[INFO] [stderr]     Checking linux-raw-sys v0.11.0
[INFO] [stderr]     Checking getrandom v0.3.3
[INFO] [stderr]     Checking once_cell v1.21.3
[INFO] [stderr]    Compiling regex v1.11.2
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking env_filter v0.1.3
[INFO] [stderr]     Checking env_logger v0.11.8
[INFO] [stderr]     Checking tempfile v3.22.0
[INFO] [stderr]     Checking nalgebra v0.33.2
[INFO] [stderr]    Compiling hts-sys v2.2.0
[INFO] [stderr]     Checking statrs v0.18.0
[INFO] [stderr]     Checking bio v2.3.0
[INFO] [stderr]     Checking rust-htslib v0.50.0
[INFO] [stderr]     Checking annorefine v2025.9.18 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 2m 34s
[INFO] running `Command { std: "docker" "inspect" "5b80078c81d9776d15e4d1e2265bde52205d6fa9848b30429127b0f24d68754d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "5b80078c81d9776d15e4d1e2265bde52205d6fa9848b30429127b0f24d68754d", kill_on_drop: false }`
[INFO] [stdout] 5b80078c81d9776d15e4d1e2265bde52205d6fa9848b30429127b0f24d68754d