[INFO] cloning repository https://github.com/davidlougheed/strkit_rust_ext [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/davidlougheed/strkit_rust_ext" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fdavidlougheed%2Fstrkit_rust_ext", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fdavidlougheed%2Fstrkit_rust_ext'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 0724ea80f73d8012aac32912d902120e8d1cba9f [INFO] testing davidlougheed/strkit_rust_ext against try#8da20828b6ea601dfd8e2448cb50ace88876bd78 for pr-150933 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fdavidlougheed%2Fstrkit_rust_ext" "/workspace/builds/worker-3-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc2/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/davidlougheed/strkit_rust_ext [INFO] finished tweaking git repo https://github.com/davidlougheed/strkit_rust_ext [INFO] tweaked toml for git repo https://github.com/davidlougheed/strkit_rust_ext written to /workspace/builds/worker-3-tc2/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/davidlougheed/strkit_rust_ext on toolchain 8da20828b6ea601dfd8e2448cb50ace88876bd78 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8da20828b6ea601dfd8e2448cb50ace88876bd78" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/davidlougheed/strkit_rust_ext 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" "+8da20828b6ea601dfd8e2448cb50ace88876bd78" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/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:cfa559dde23f44738f9990739aaa3487d8df3af37eb5df0572f7cf76004a604a" "/opt/rustwide/cargo-home/bin/cargo" "+8da20828b6ea601dfd8e2448cb50ace88876bd78" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] b461de2b839bceaa7a4243c807b284c1c865a3d88d2f2992855affbcdf2db748 [INFO] running `Command { std: "docker" "start" "-a" "b461de2b839bceaa7a4243c807b284c1c865a3d88d2f2992855affbcdf2db748", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "b461de2b839bceaa7a4243c807b284c1c865a3d88d2f2992855affbcdf2db748", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b461de2b839bceaa7a4243c807b284c1c865a3d88d2f2992855affbcdf2db748", kill_on_drop: false }` [INFO] [stdout] b461de2b839bceaa7a4243c807b284c1c865a3d88d2f2992855affbcdf2db748 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/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:cfa559dde23f44738f9990739aaa3487d8df3af37eb5df0572f7cf76004a604a" "/opt/rustwide/cargo-home/bin/cargo" "+8da20828b6ea601dfd8e2448cb50ace88876bd78" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 8fd5453691ad016353bff92f608158755baeac794fefadab3a28f42a59c88317 [INFO] running `Command { std: "docker" "start" "-a" "8fd5453691ad016353bff92f608158755baeac794fefadab3a28f42a59c88317", kill_on_drop: false }` [INFO] [stderr] Compiling memchr v2.8.0 [INFO] [stderr] Compiling libm v0.2.16 [INFO] [stderr] Compiling target-lexicon v0.13.5 [INFO] [stderr] Compiling python3-dll-a v0.2.14 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling minimal-lexical v0.2.1 [INFO] [stderr] Compiling regex-syntax v0.8.10 [INFO] [stderr] Compiling libloading v0.8.9 [INFO] [stderr] Compiling matrixmultiply v0.3.10 [INFO] [stderr] Compiling syn v2.0.117 [INFO] [stderr] Compiling prettyplease v0.2.37 [INFO] [stderr] Compiling bindgen v0.69.5 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling bytemuck v1.25.0 [INFO] [stderr] Compiling bindgen v0.72.1 [INFO] [stderr] Compiling libz-sys v1.1.24 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling bzip2-sys v0.1.13+1.0.8 [INFO] [stderr] Compiling libdeflate-sys v1.25.2 [INFO] [stderr] Compiling safe_arch v0.7.4 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling itertools v0.13.0 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling aho-corasick v1.1.4 [INFO] [stderr] Compiling pyo3-build-config v0.28.2 [INFO] [stderr] Compiling rand_core v0.9.5 [INFO] [stderr] Compiling wide v0.7.33 [INFO] [stderr] Compiling percent-encoding v2.3.2 [INFO] [stderr] Compiling form_urlencoded v1.2.2 [INFO] [stderr] Compiling rand_chacha v0.9.0 [INFO] [stderr] Compiling regex-automata v0.4.14 [INFO] [stderr] Compiling csv-core v0.1.13 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling bit-vec v0.8.0 [INFO] [stderr] Compiling fixedbitset v0.5.7 [INFO] [stderr] Compiling csv v1.4.0 [INFO] [stderr] Compiling petgraph v0.7.1 [INFO] [stderr] Compiling bit-set v0.8.0 [INFO] [stderr] Compiling rand v0.9.2 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling bytecount v0.6.9 [INFO] [stderr] Compiling cexpr v0.6.0 [INFO] [stderr] Compiling num-complex v0.4.6 [INFO] [stderr] Compiling num-integer v0.1.46 [INFO] [stderr] Compiling regex v1.12.3 [INFO] [stderr] Compiling pyo3-ffi v0.28.2 [INFO] [stderr] Compiling pyo3-macros-backend v0.28.2 [INFO] [stderr] Compiling approx v0.5.1 [INFO] [stderr] Compiling num-rational v0.4.2 [INFO] [stderr] Compiling pyo3 v0.28.2 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling numpy v0.28.0 [INFO] [stderr] Compiling simba v0.9.1 [INFO] [stderr] Compiling ndarray v0.16.1 [INFO] [stderr] Compiling ndarray v0.17.2 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling ordered-float v5.1.0 [INFO] [stderr] Compiling editdistancek v1.0.2 [INFO] [stderr] Compiling triple_accel v0.4.0 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling rust-lapper v1.2.0 [INFO] [stderr] Compiling synstructure v0.13.2 [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 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 strum_macros v0.26.4 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling derive_more-impl v2.1.1 [INFO] [stderr] Compiling derive-new v0.7.0 [INFO] [stderr] Compiling enum-map v2.7.3 [INFO] [stderr] Compiling zerofrom v0.1.6 [INFO] [stderr] Compiling thiserror v1.0.69 [INFO] [stderr] Compiling thiserror v2.0.18 [INFO] [stderr] Compiling yoke v0.8.1 [INFO] [stderr] Compiling derive_more v2.1.1 [INFO] [stderr] Compiling zerovec v0.11.5 [INFO] [stderr] Compiling zerotrie v0.2.3 [INFO] [stderr] Compiling bio-types v1.0.4 [INFO] [stderr] Compiling tinystr v0.8.2 [INFO] [stderr] Compiling potential_utf v0.1.4 [INFO] [stderr] Compiling icu_locale_core v2.1.1 [INFO] [stderr] Compiling icu_collections v2.1.1 [INFO] [stderr] Compiling serde v1.0.228 [INFO] [stderr] Compiling icu_provider v2.1.1 [INFO] [stderr] Compiling icu_normalizer v2.1.1 [INFO] [stderr] Compiling icu_properties v2.1.2 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling multimap v0.10.1 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling bincode v2.0.1 [INFO] [stderr] Compiling pyo3-macros v0.28.2 [INFO] [stderr] Compiling hts-sys v2.2.0 [INFO] [stderr] Compiling nalgebra v0.33.2 [INFO] [stderr] Compiling idna_adapter v1.2.1 [INFO] [stderr] Compiling idna v1.1.0 [INFO] [stderr] Compiling url v2.5.8 [INFO] [stderr] Compiling libparasail-sys v0.2.0 [INFO] [stderr] Compiling rust-htslib v1.0.0 [INFO] [stderr] Compiling statrs v0.18.0 [INFO] [stderr] Compiling bio v2.2.0 [INFO] [stderr] Compiling parasail-rs v0.9.0 [INFO] [stderr] Compiling strkit_rust_ext v0.26.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: field `contig_names` is never read [INFO] [stdout] --> src/strkit/reads.rs:528:5 [INFO] [stdout] | [INFO] [stdout] 521 | pub struct STRkitBAMReader { [INFO] [stdout] | --------------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 528 | contig_names: Vec, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `sample_idx` is never read [INFO] [stdout] --> src/strkit/snvs.rs:113:5 [INFO] [stdout] | [INFO] [stdout] 107 | pub struct STRkitVCFReader { [INFO] [stdout] | --------------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 113 | sample_idx: Option, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 5m 26s [INFO] running `Command { std: "docker" "inspect" "8fd5453691ad016353bff92f608158755baeac794fefadab3a28f42a59c88317", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8fd5453691ad016353bff92f608158755baeac794fefadab3a28f42a59c88317", kill_on_drop: false }` [INFO] [stdout] 8fd5453691ad016353bff92f608158755baeac794fefadab3a28f42a59c88317 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/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:cfa559dde23f44738f9990739aaa3487d8df3af37eb5df0572f7cf76004a604a" "/opt/rustwide/cargo-home/bin/cargo" "+8da20828b6ea601dfd8e2448cb50ace88876bd78" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 70cebca2321292e97eaca0ded79aa076fdbed138a8a13d81fc886665cd925d09 [INFO] running `Command { std: "docker" "start" "-a" "70cebca2321292e97eaca0ded79aa076fdbed138a8a13d81fc886665cd925d09", kill_on_drop: false }` [INFO] [stderr] Compiling strkit_rust_ext v0.26.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: field `contig_names` is never read [INFO] [stdout] --> src/strkit/reads.rs:528:5 [INFO] [stdout] | [INFO] [stdout] 521 | pub struct STRkitBAMReader { [INFO] [stdout] | --------------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 528 | contig_names: Vec, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `sample_idx` is never read [INFO] [stdout] --> src/strkit/snvs.rs:113:5 [INFO] [stdout] | [INFO] [stdout] 107 | pub struct STRkitVCFReader { [INFO] [stdout] | --------------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 113 | sample_idx: Option, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 4.66s [INFO] running `Command { std: "docker" "inspect" "70cebca2321292e97eaca0ded79aa076fdbed138a8a13d81fc886665cd925d09", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "70cebca2321292e97eaca0ded79aa076fdbed138a8a13d81fc886665cd925d09", kill_on_drop: false }` [INFO] [stdout] 70cebca2321292e97eaca0ded79aa076fdbed138a8a13d81fc886665cd925d09 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/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:cfa559dde23f44738f9990739aaa3487d8df3af37eb5df0572f7cf76004a604a" "/opt/rustwide/cargo-home/bin/cargo" "+8da20828b6ea601dfd8e2448cb50ace88876bd78" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] da2daf3912a77cc5f1cfccf4298d5ddfa3083712eaf4f49f55291bff7fa0862f [INFO] running `Command { std: "docker" "start" "-a" "da2daf3912a77cc5f1cfccf4298d5ddfa3083712eaf4f49f55291bff7fa0862f", kill_on_drop: false }` [INFO] [stderr] warning: field `contig_names` is never read [INFO] [stderr] --> src/strkit/reads.rs:528:5 [INFO] [stderr] | [INFO] [stderr] 521 | pub struct STRkitBAMReader { [INFO] [stderr] | --------------- field in this struct [INFO] [stderr] ... [INFO] [stderr] 528 | contig_names: Vec, [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: field `sample_idx` is never read [INFO] [stderr] --> src/strkit/snvs.rs:113:5 [INFO] [stderr] | [INFO] [stderr] 107 | pub struct STRkitVCFReader { [INFO] [stderr] | --------------- field in this struct [INFO] [stderr] ... [INFO] [stderr] 113 | sample_idx: Option, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: `strkit_rust_ext` (lib test) generated 2 warnings [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.23s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/strkit_rust_ext-fc70d029ab391803) [INFO] [stdout] [INFO] [stdout] running 7 tests [INFO] [stdout] test strkit::consensus::best_representatives::test::test_best_representative ... ok [INFO] [stdout] test strkit::consensus::best_representatives::test::test_best_representatives ... ok [INFO] [stdout] test strkit::utils::test::test_calc_motif_size_kmers ... ok [INFO] [stdout] test strkit::utils::test::test_starts_with_chr ... ok [INFO] [stdout] test strkit::utils::test::test_normalize_contig ... ok [INFO] [stdout] test strkit::consensus::poa::test::test_poa_consensus_seq ... ok [INFO] [stdout] test strkit::consensus::best_representatives::test::test_seqs_summed_levenshtein_similarity ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.28s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "da2daf3912a77cc5f1cfccf4298d5ddfa3083712eaf4f49f55291bff7fa0862f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "da2daf3912a77cc5f1cfccf4298d5ddfa3083712eaf4f49f55291bff7fa0862f", kill_on_drop: false }` [INFO] [stdout] da2daf3912a77cc5f1cfccf4298d5ddfa3083712eaf4f49f55291bff7fa0862f