[INFO] fetching crate gecco 0.5.5...
[INFO] checking gecco-0.5.5 against 4fcf39725a9c99bd495d8c73af83628a256ff9a9 for pr-162233-crater-rollup
[INFO] extracting crate gecco 0.5.5 into /workspace/builds/worker-0-tc1/source
[INFO] started tweaking crates.io crate gecco 0.5.5
[INFO] removed 0 missing tests
[INFO] finished tweaking crates.io crate gecco 0.5.5
[INFO] tweaked toml for crates.io crate gecco 0.5.5 written to /workspace/builds/worker-0-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate gecco 0.5.5 on toolchain 4fcf39725a9c99bd495d8c73af83628a256ff9a9
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+4fcf39725a9c99bd495d8c73af83628a256ff9a9" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate gecco 0.5.5 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" "+4fcf39725a9c99bd495d8c73af83628a256ff9a9" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr] warning: explicit `package.readme` can be inferred
[INFO] [stderr]    --> Cargo.toml:139:1
[INFO] [stderr]     |
[INFO] [stderr] 139 | readme = "README.md"
[INFO] [stderr]     | ^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `cargo::manual_readme` is set to `warn` by default
[INFO] [stderr] help: consider removing `package.readme`
[INFO] [stderr] warning: binary `bench_full` should have a kebab-case name
[INFO] [stderr]   |
[INFO] [stderr] 1 | /workspace/builds/worker-0-tc1/source/target/.../bench_full
[INFO] [stderr]   |                                                  ^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `cargo::non_kebab_case_bins` is set to `warn` by default
[INFO] [stderr] help: to change the binary name to `bench-full`, convert `bin.name`
[INFO] [stderr]  --> Cargo.toml:2:8
[INFO] [stderr]   |
[INFO] [stderr] 2 - name = "bench_full"
[INFO] [stderr] 2 + name = "bench-full"
[INFO] [stderr]   |
[INFO] [stderr] warning: binary `bench_pipeline` should have a kebab-case name
[INFO] [stderr]   |
[INFO] [stderr] 1 | /workspace/builds/worker-0-tc1/source/target/.../bench_pipeline
[INFO] [stderr]   |                                                  ^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr] help: to change the binary name to `bench-pipeline`, convert `bin.name`
[INFO] [stderr]  --> Cargo.toml:7:8
[INFO] [stderr]   |
[INFO] [stderr] 7 - name = "bench_pipeline"
[INFO] [stderr] 7 + name = "bench-pipeline"
[INFO] [stderr]   |
[INFO] [stderr] warning: `package.homepage` is redundant with `package.repository`
[INFO] [stderr]    --> Cargo.toml:134:12
[INFO] [stderr]     |
[INFO] [stderr] 134 | homepage = "https://github.com/henriksson-lab/gecco-rs"
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] ...
[INFO] [stderr] 140 | repository = "https://github.com/henriksson-lab/gecco-rs"
[INFO] [stderr]     |              --------------------------------------------
[INFO] [stderr]     |
[INFO] [stderr]     = note: `cargo::redundant_homepage` is set to `warn` by default
[INFO] [stderr] help: consider removing `package.homepage`
[INFO] [stderr] warning: `gecco` (manifest) generated 4 warnings
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded sacabase v2.0.0
[INFO] [stderr]   Downloaded derefable v0.1.0
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded enum-map-derive v0.17.0
[INFO] [stderr]   Downloaded derive-new v0.6.0
[INFO] [stderr]   Downloaded circular v0.3.0
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded noodles-bgzf v0.47.0
[INFO] [stderr]   Downloaded noodles-fasta v0.62.0
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded alga v0.9.3
[INFO] [stderr]   Downloaded enum-map v2.7.3
[INFO] [stderr]   Downloaded bit-set v0.10.0
[INFO] [stderr]   Downloaded gb-io v0.9.0
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded indicatif v0.18.5
[INFO] [stderr]   Downloaded jiff-static v0.2.31
[INFO] [stderr]   Downloaded crfsuite-compliant-rs v0.4.1
[INFO] [stderr]   Downloaded zlib-rs v0.6.4
[INFO] [stderr]   Downloaded liblbfgs-compliant-rs v0.1.5
[INFO] [stderr]   Downloaded bio v4.0.1
[INFO] [stderr]   Downloaded divsufsort v2.0.0
[INFO] [stderr]   Downloaded prodigal-rs v0.3.5
[INFO] [stderr]   Downloaded jiff v0.2.31
[INFO] [stderr]   Downloaded hmmer-pure-rs v0.7.4
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:8683fc1fc2eb5c9ac98e0d076ab094b2ffac7f99da555d2b6a2e27f346de2ec7" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] c69c240a7f54fe5c9785530c6789b8ca0138b6b56750835c0e520ec47e5c25bf
[INFO] running `Command { std: "docker" "start" "c69c240a7f54fe5c9785530c6789b8ca0138b6b56750835c0e520ec47e5c25bf", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "c69c240a7f54fe5c9785530c6789b8ca0138b6b56750835c0e520ec47e5c25bf", 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" "c69c240a7f54fe5c9785530c6789b8ca0138b6b56750835c0e520ec47e5c25bf" "/opt/rustwide/cargo-home/bin/cargo" "+4fcf39725a9c99bd495d8c73af83628a256ff9a9" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "c69c240a7f54fe5c9785530c6789b8ca0138b6b56750835c0e520ec47e5c25bf", 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" "c69c240a7f54fe5c9785530c6789b8ca0138b6b56750835c0e520ec47e5c25bf" "/opt/rustwide/cargo-home/bin/cargo" "+4fcf39725a9c99bd495d8c73af83628a256ff9a9" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr] warning: explicit `package.readme` can be inferred
[INFO] [stderr]    --> Cargo.toml:139:1
[INFO] [stderr]     |
[INFO] [stderr] 139 | readme = "README.md"
[INFO] [stderr]     | ^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `cargo::manual_readme` is set to `warn` by default
[INFO] [stderr] help: consider removing `package.readme`
[INFO] [stderr] warning: binary `bench_full` should have a kebab-case name
[INFO] [stderr]   |
[INFO] [stderr] 1 | /opt/rustwide/target/.../bench_full
[INFO] [stderr]   |                          ^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `cargo::non_kebab_case_bins` is set to `warn` by default
[INFO] [stderr] help: to change the binary name to `bench-full`, convert `bin.name`
[INFO] [stderr]  --> Cargo.toml:2:8
[INFO] [stderr]   |
[INFO] [stderr] 2 - name = "bench_full"
[INFO] [stderr] 2 + name = "bench-full"
[INFO] [stderr]   |
[INFO] [stderr] warning: binary `bench_pipeline` should have a kebab-case name
[INFO] [stderr]   |
[INFO] [stderr] 1 | /opt/rustwide/target/.../bench_pipeline
[INFO] [stderr]   |                          ^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr] help: to change the binary name to `bench-pipeline`, convert `bin.name`
[INFO] [stderr]  --> Cargo.toml:7:8
[INFO] [stderr]   |
[INFO] [stderr] 7 - name = "bench_pipeline"
[INFO] [stderr] 7 + name = "bench-pipeline"
[INFO] [stderr]   |
[INFO] [stderr] warning: `package.homepage` is redundant with `package.repository`
[INFO] [stderr]    --> Cargo.toml:134:12
[INFO] [stderr]     |
[INFO] [stderr] 134 | homepage = "https://github.com/henriksson-lab/gecco-rs"
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] ...
[INFO] [stderr] 140 | repository = "https://github.com/henriksson-lab/gecco-rs"
[INFO] [stderr]     |              --------------------------------------------
[INFO] [stderr]     |
[INFO] [stderr]     = note: `cargo::redundant_homepage` is set to `warn` by default
[INFO] [stderr] help: consider removing `package.homepage`
[INFO] [stderr] warning: `gecco` (manifest) generated 4 warnings
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling cc v1.2.65
[INFO] [stderr]    Compiling serde_core v1.0.228
[INFO] [stderr]    Compiling httparse v1.10.1
[INFO] [stderr]    Compiling matrixmultiply v0.3.10
[INFO] [stderr]    Compiling native-tls v0.2.18
[INFO] [stderr]    Compiling syn v2.0.118
[INFO] [stderr]     Checking getrandom v0.2.17
[INFO] [stderr]     Checking zlib-rs v0.6.4
[INFO] [stderr]     Checking ppv-lite86 v0.2.21
[INFO] [stderr]     Checking aho-corasick v1.1.4
[INFO] [stderr]     Checking bytemuck v1.25.0
[INFO] [stderr]    Compiling zeroize v1.9.0
[INFO] [stderr]    Compiling proc-macro2 v0.4.30
[INFO] [stderr]    Compiling foreign-types-shared v0.1.1
[INFO] [stderr]    Compiling simd-adler32 v0.3.9
[INFO] [stderr]    Compiling foreign-types v0.3.2
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling bytes v1.12.0
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]    Compiling unicode-xid v0.1.0
[INFO] [stderr]    Compiling adler2 v2.0.1
[INFO] [stderr]    Compiling pem-rfc7468 v1.0.0
[INFO] [stderr]    Compiling miniz_oxide v0.8.9
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling rustls-pki-types v1.14.1
[INFO] [stderr]     Checking safe_arch v0.7.4
[INFO] [stderr]    Compiling crc32fast v1.5.0
[INFO] [stderr]    Compiling num-complex v0.2.4
[INFO] [stderr]    Compiling syn v0.15.44
[INFO] [stderr]    Compiling openssl-probe v0.2.1
[INFO] [stderr]    Compiling base64 v0.22.1
[INFO] [stderr]    Compiling const-oid v0.10.2
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]    Compiling flate2 v1.1.9
[INFO] [stderr]     Checking wide v0.7.33
[INFO] [stderr]    Compiling digest v0.11.3
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking rand v0.8.6
[INFO] [stderr]     Checking rayon v1.12.0
[INFO] [stderr]    Compiling der v0.8.1
[INFO] [stderr]    Compiling http v1.4.2
[INFO] [stderr]    Compiling webpki-root-certs v1.0.9
[INFO] [stderr]    Compiling quote v0.6.13
[INFO] [stderr]    Compiling liblbfgs-compliant-rs v0.1.5
[INFO] [stderr]    Compiling utf8-zero v0.8.1
[INFO] [stderr]    Compiling sha2 v0.11.0
[INFO] [stderr]     Checking regex-automata v0.4.14
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking approx v0.3.2
[INFO] [stderr]     Checking sacabase v2.0.0
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]     Checking csv-core v0.1.13
[INFO] [stderr]     Checking bstr v1.12.3
[INFO] [stderr]     Checking fixedbitset v0.5.7
[INFO] [stderr]     Checking bumpalo v3.20.3
[INFO] [stderr]     Checking bit-vec v0.9.1
[INFO] [stderr]     Checking ndarray v0.17.2
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking petgraph v0.8.3
[INFO] [stderr]    Compiling ureq-proto v0.6.0
[INFO] [stderr]     Checking zopfli v0.8.3
[INFO] [stderr]     Checking bit-set v0.10.0
[INFO] [stderr]     Checking noodles-core v0.20.0
[INFO] [stderr]    Compiling openssl-sys v0.9.117
[INFO] [stderr]     Checking console v0.16.3
[INFO] [stderr]     Checking alga v0.9.3
[INFO] [stderr]     Checking noodles-bgzf v0.47.0
[INFO] [stderr]     Checking divsufsort v2.0.0
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v5.3.0
[INFO] [stderr]     Checking simba v0.9.1
[INFO] [stderr]     Checking socket2 v0.5.10
[INFO] [stderr]     Checking num_cpus v1.17.0
[INFO] [stderr]    Compiling openssl v0.10.81
[INFO] [stderr]     Checking csv v1.4.0
[INFO] [stderr]     Checking memmap2 v0.9.11
[INFO] [stderr]     Checking itertools v0.14.0
[INFO] [stderr]     Checking itertools v0.15.0
[INFO] [stderr]     Checking nom v8.0.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking strum v0.28.0
[INFO] [stderr]     Checking bytecount v0.6.9
[INFO] [stderr]     Checking circular v0.3.0
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking typed-path v0.12.3
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking unit-prefix v0.5.2
[INFO] [stderr]     Checking jiff v0.2.31
[INFO] [stderr]     Checking indicatif v0.18.5
[INFO] [stderr]     Checking serde_json v1.0.150
[INFO] [stderr]     Checking rand v0.10.1
[INFO] [stderr]    Compiling derefable v0.1.0
[INFO] [stderr]     Checking noodles-fasta v0.62.0
[INFO] [stderr]     Checking quick-xml v0.41.0
[INFO] [stderr]     Checking md5 v0.8.0
[INFO] [stderr]     Checking regex v1.12.4
[INFO] [stderr]     Checking env_filter v2.0.0
[INFO] [stderr]     Checking zip v8.6.0
[INFO] [stderr]    Compiling openssl-macros v0.1.1
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling thiserror-impl v2.0.18
[INFO] [stderr]    Compiling clap_derive v4.6.1
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling strum_macros v0.28.0
[INFO] [stderr]    Compiling getset v0.1.7
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]     Checking thiserror v2.0.18
[INFO] [stderr]     Checking thiserror v1.0.69
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking env_logger v0.11.11
[INFO] [stderr]     Checking clap v4.6.1
[INFO] [stderr]     Checking hmmer-pure-rs v0.7.4
[INFO] [stderr]     Checking crfsuite-compliant-rs v0.4.1
[INFO] [stderr]     Checking prodigal-rs v0.3.5
[INFO] [stderr]     Checking nalgebra v0.33.3
[INFO] [stderr]     Checking sprs v0.11.4
[INFO] [stderr]     Checking gb-io v0.9.0
[INFO] [stderr]     Checking serde v1.0.228
[INFO] [stderr]     Checking multimap v0.10.1
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking ureq v3.3.0
[INFO] [stderr]    Compiling gecco v0.5.5 (/opt/rustwide/workdir)
[INFO] [stderr]     Checking statrs v0.18.0
[INFO] [stderr]     Checking bio v4.0.1
[INFO] [stderr] warning: unused dependency `bio`
[INFO] [stderr]   --> Cargo.toml:30:15
[INFO] [stderr]    |
[INFO] [stderr] 30 | [dependencies.bio]
[INFO] [stderr]    |               ^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `cargo::unused_dependencies` is set to `warn` by default
[INFO] [stderr] help: consider removing the dependency on `bio`
[INFO] [stderr] warning: unused dependency `indicatif`
[INFO] [stderr]   --> Cargo.toml:58:15
[INFO] [stderr]    |
[INFO] [stderr] 58 | [dependencies.indicatif]
[INFO] [stderr]    |               ^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `indicatif`
[INFO] [stderr] warning: unused dependency `noodles-fasta`
[INFO] [stderr]   --> Cargo.toml:71:15
[INFO] [stderr]    |
[INFO] [stderr] 71 | [dependencies.noodles-fasta]
[INFO] [stderr]    |               ^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `noodles-fasta`
[INFO] [stderr] warning: unused dependency `sprs`
[INFO] [stderr]   --> Cargo.toml:96:15
[INFO] [stderr]    |
[INFO] [stderr] 96 | [dependencies.sprs]
[INFO] [stderr]    |               ^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `sprs`
[INFO] [stderr] warning: `gecco` (manifest) generated 4 warnings
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 15s
[INFO] running `Command { std: "docker" "inspect" "c69c240a7f54fe5c9785530c6789b8ca0138b6b56750835c0e520ec47e5c25bf", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c69c240a7f54fe5c9785530c6789b8ca0138b6b56750835c0e520ec47e5c25bf", kill_on_drop: false }`
[INFO] [stdout] c69c240a7f54fe5c9785530c6789b8ca0138b6b56750835c0e520ec47e5c25bf
