[INFO] cloning repository https://github.com/earth-metabolome-initiative/spectral-matcher [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/earth-metabolome-initiative/spectral-matcher" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fearth-metabolome-initiative%2Fspectral-matcher", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fearth-metabolome-initiative%2Fspectral-matcher'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 5a50d623c68543daf79cc4125d482a27308f9017 [INFO] testing earth-metabolome-initiative/spectral-matcher against 1.99.0-beta.1+cargoflags=--release for beta-release-1.99-2 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fearth-metabolome-initiative%2Fspectral-matcher" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/earth-metabolome-initiative/spectral-matcher [INFO] finished tweaking git repo https://github.com/earth-metabolome-initiative/spectral-matcher [INFO] tweaked toml for git repo https://github.com/earth-metabolome-initiative/spectral-matcher written to /workspace/builds/worker-6-tc2/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/earth-metabolome-initiative/spectral-matcher on toolchain 1.99.0-beta.1 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.99.0-beta.1" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/earth-metabolome-initiative/spectral-matcher 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" "+1.99.0-beta.1" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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] f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517 [INFO] running `Command { std: "docker" "start" "f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517", 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" "f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.1" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517", 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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.1" "build" "--frozen" "--message-format=json" "--release", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.184 [INFO] [stderr] Compiling wasm-bindgen-shared v0.2.117 [INFO] [stderr] Compiling quote v1.0.45 [INFO] [stderr] Compiling serde_core v1.0.228 [INFO] [stderr] Compiling futures-sink v0.3.32 [INFO] [stderr] Compiling cc v1.2.59 [INFO] [stderr] Compiling writeable v0.6.3 [INFO] [stderr] Compiling litemap v0.8.2 [INFO] [stderr] Compiling futures-util v0.3.32 [INFO] [stderr] Compiling icu_normalizer_data v2.2.0 [INFO] [stderr] Compiling icu_properties_data v2.2.0 [INFO] [stderr] Compiling syn v2.0.117 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling typenum v1.20.1 [INFO] [stderr] Compiling wasm-bindgen v0.2.117 [INFO] [stderr] Compiling radium v0.7.0 [INFO] [stderr] Compiling rustls v0.23.37 [INFO] [stderr] Compiling thiserror v2.0.18 [INFO] [stderr] Compiling generic-array v0.14.7 [INFO] [stderr] Compiling ring v0.17.14 [INFO] [stderr] Compiling futures-channel v0.3.32 [INFO] [stderr] Compiling socket2 v0.6.3 [INFO] [stderr] Compiling mio v1.2.0 [INFO] [stderr] Compiling getrandom v0.2.17 [INFO] [stderr] Compiling tokio v1.51.1 [INFO] [stderr] Compiling tracing-core v0.1.36 [INFO] [stderr] Compiling zerocopy v0.8.48 [INFO] [stderr] Compiling tap v1.0.1 [INFO] [stderr] Compiling wyz v0.5.1 [INFO] [stderr] Compiling block-buffer v0.10.4 [INFO] [stderr] Compiling crypto-common v0.1.7 [INFO] [stderr] Compiling tracing v0.1.44 [INFO] [stderr] Compiling rand_core v0.10.1 [INFO] [stderr] Compiling stable_try_trait_v2 v1.75.1 [INFO] [stderr] Compiling aliasable v0.1.3 [INFO] [stderr] Compiling funty v2.0.0 [INFO] [stderr] Compiling fallible-iterator v0.3.0 [INFO] [stderr] Compiling maybe-dangling v0.1.2 [INFO] [stderr] Compiling portable-atomic v1.13.1 [INFO] [stderr] Compiling indexmap v2.13.1 [INFO] [stderr] Compiling lender v0.6.2 [INFO] [stderr] Compiling rand v0.10.1 [INFO] [stderr] Compiling digest v0.10.7 [INFO] [stderr] Compiling bitvec v1.0.1 [INFO] [stderr] Compiling webpki-roots v1.0.6 [INFO] [stderr] Compiling winnow v0.7.15 [INFO] [stderr] Compiling toml_write v0.1.2 [INFO] [stderr] Compiling litrs v1.0.0 [INFO] [stderr] Compiling synstructure v0.13.2 [INFO] [stderr] Compiling wasm-bindgen-macro-support v0.2.117 [INFO] [stderr] Compiling iri-string v0.7.12 [INFO] [stderr] Compiling zerofrom-derive v0.1.7 [INFO] [stderr] Compiling yoke-derive v0.8.2 [INFO] [stderr] Compiling zerofrom v0.1.7 [INFO] [stderr] Compiling zerovec-derive v0.11.3 [INFO] [stderr] Compiling yoke v0.8.2 [INFO] [stderr] Compiling displaydoc v0.2.5 [INFO] [stderr] Compiling serde_derive v1.0.228 [INFO] [stderr] Compiling thiserror-impl v2.0.18 [INFO] [stderr] Compiling zerotrie v0.2.4 [INFO] [stderr] Compiling hyper v1.9.0 [INFO] [stderr] Compiling zerovec v0.11.6 [INFO] [stderr] Compiling zerocopy-derive v0.8.48 [INFO] [stderr] Compiling tinystr v0.8.3 [INFO] [stderr] Compiling icu_locale_core v2.2.0 [INFO] [stderr] Compiling potential_utf v0.1.5 [INFO] [stderr] Compiling icu_collections v2.2.0 [INFO] [stderr] Compiling wasm-bindgen-macro v0.2.117 [INFO] [stderr] Compiling hyper-util v0.1.20 [INFO] [stderr] Compiling serde v1.0.228 [INFO] [stderr] Compiling icu_provider v2.2.0 [INFO] [stderr] Compiling icu_normalizer v2.2.0 [INFO] [stderr] Compiling icu_properties v2.2.0 [INFO] [stderr] Compiling toml_datetime v0.6.11 [INFO] [stderr] Compiling serde_spanned v0.6.9 [INFO] [stderr] Compiling js-sys v0.3.94 [INFO] [stderr] Compiling multi_ranged v0.1.2 [INFO] [stderr] Compiling tower v0.5.3 [INFO] [stderr] Compiling sha2 v0.10.9 [INFO] [stderr] Compiling console v0.15.11 [INFO] [stderr] Compiling geometric-traits v0.1.0 (https://github.com/earth-metabolome-initiative/geometric-traits#23000558) [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 rustls-webpki v0.103.10 [INFO] [stderr] Compiling tower-http v0.6.8 [INFO] [stderr] Compiling toml_edit v0.22.27 [INFO] [stderr] Compiling half v2.7.1 [INFO] [stderr] Compiling serde_urlencoded v0.7.1 [INFO] [stderr] Compiling document-features v0.2.12 [INFO] [stderr] Compiling serde_json v1.0.149 [INFO] [stderr] Compiling csv-core v0.1.13 [INFO] [stderr] Compiling number_prefix v0.4.0 [INFO] [stderr] Compiling arbitrary v1.4.2 [INFO] [stderr] Compiling csv v1.4.0 [INFO] [stderr] Compiling indicatif v0.17.11 [INFO] [stderr] Compiling toml v0.8.23 [INFO] [stderr] Compiling wasm-bindgen-futures v0.4.67 [INFO] [stderr] Compiling poll-promise v0.3.0 [INFO] [stderr] Compiling tokio-rustls v0.26.4 [INFO] [stderr] Compiling hyper-rustls v0.27.7 [INFO] [stderr] Compiling reqwest v0.12.28 [INFO] [stderr] Compiling mass_spectrometry v0.1.0 (https://github.com/earth-metabolome-initiative/mass-spectrometry-traits#36010634) [INFO] [stderr] Compiling spectral-matcher v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `release` profile [optimized] target(s) in 4m 14s [INFO] running `Command { std: "docker" "inspect" "f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517", 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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.1" "test" "--frozen" "--no-run" "--message-format=json" "--release", kill_on_drop: false }` [INFO] [stderr] Compiling spectral-matcher v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `release` profile [optimized] target(s) in 33.68s [INFO] running `Command { std: "docker" "inspect" "f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517", 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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.1" "test" "--frozen" "--release", kill_on_drop: false }` [INFO] [stderr] Finished `release` profile [optimized] target(s) in 0.22s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/release/deps/spectral_matcher-5bca903e24229b4d) [INFO] [stdout] [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/release/deps/spectral_matcher-9c2387d2fdeffd57) [INFO] [stdout] running 31 tests [INFO] [stderr] Running tests/api.rs (/opt/rustwide/target/release/deps/api-b51c05831dba0db1) [INFO] [stdout] test consensus::tests::cross_library_consensus_can_beat_singleton_top_hit ... ok [INFO] [stdout] test consensus::tests::duplicate_hits_in_one_library_are_collapsed_before_scoring ... ok [INFO] [stdout] test consensus::tests::out_of_window_consensus_does_not_override_singleton ... ok [INFO] [stdout] test consensus::tests::singleton_is_retained_when_only_one_library_supports_query ... ok [INFO] [stdout] test export::tests::search_json_exports_rows ... ok [INFO] [stdout] test databases::tests::resolve_database_accepts_id_name_and_filename ... ok [INFO] [stdout] test export::tests::search_tsv_includes_taxonomy_columns_when_reranking_is_applied ... ok [INFO] [stdout] test export::tests::search_tsv_exports_one_row_per_hit_with_dynamic_headers ... ok [INFO] [stdout] test network::tests::selected_neighbor_build_matches_pair_score_build ... ok [INFO] [stdout] test network::tests::threshold_and_topk_with_or_rule_keeps_expected_edges ... ok [INFO] [stdout] test mgf::tests::keeps_fixed_fields_alongside_headers ... ok [INFO] [stdout] test mgf::tests::preserves_arbitrary_headers_with_normalized_keys ... ok [INFO] [stdout] test mgf::tests::rejects_duplicate_spectrum_ids ... ok [INFO] [stdout] test search::tests::indexed_network_neighbors_match_scalar_linear_cosine ... ok [INFO] [stdout] test search::tests::run_search_request_accepts_genus_level_taxonomic_queries ... ok [INFO] [stdout] test search::tests::incremental_search_applies_filters_and_top_n ... ok [INFO] [stdout] test search::tests::native_search_matches_incremental_result_shape ... ok [INFO] [stdout] test search::tests::run_search_request_applies_taxonomic_reranking_before_final_top_n ... ok [INFO] [stdout] test search::tests::search_candidate_sorting_uses_score_matches_then_library_index ... ok [INFO] [stdout] test consensus::tests::mixed_full_structures_are_marked_as_short_inchikey_consensus ... ok [INFO] [stdout] test search::tests::search_respects_precursor_mz_tolerance ... ok [INFO] [stdout] test server::tests::raw_response_contains_content_length ... ok [INFO] [stdout] test similarity::tests::linear_cosine_preprocessing_merges_close_peaks ... ok [INFO] [stdout] test similarity::tests::top_n_peak_filter_keeps_most_intense_peaks_for_similarity_only ... ok [INFO] [stdout] test taxonomy::tests::otol_validation_accepts_exact_non_synonym ... ok [INFO] [stdout] test similarity::tests::modified_linear_cosine_preprocessing_merges_close_peaks ... ok [INFO] [stdout] test taxonomy::tests::resolves_query_lineage_by_name_qid_and_genus ... ok [INFO] [stdout] test taxonomy::tests::otol_validation_rejects_approximate_match ... ok [INFO] [stdout] test taxonomy::tests::otol_validation_rejects_synonym_with_corrected_match ... ok [INFO] [stdout] test consensus::tests::query_order_is_preserved_and_empty_queries_are_kept ... ok [INFO] [stdout] test network::tests::component_selection_reports_largest_component ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 31 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] running 4 tests [INFO] [stdout] test network_build_accepts_missing_precursor_mz_but_default_parsing_drops_it ... ok [INFO] [stdout] test search_can_infer_missing_precursor_mz_from_highest_fragment_mz ... ok [INFO] [stdout] test async_search_job_endpoints_work ... ok [INFO] [stdout] test health_and_sync_network_endpoints_work ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 4 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.10s [INFO] [stdout] [INFO] [stderr] Running tests/cli.rs (/opt/rustwide/target/release/deps/cli-68c32547a2583fae) [INFO] [stdout] [INFO] [stdout] running 7 tests [INFO] [stdout] test metrics_cli_lists_available_metrics ... ok [INFO] [stdout] test db_list_cli_lists_seeded_databases ... ok [INFO] [stdout] test consensus_cli_merges_two_search_artifacts_into_one_annotation_per_query ... ok [INFO] [stdout] test search_cli_applies_taxonomic_reranking_when_taxonomy_config_is_present ... ok [INFO] [stdout] test network_cli_writes_network_json_and_csvs ... ok [INFO] [stdout] test search_cli_writes_json_and_optional_tsv ... ok [INFO] [stderr] Doc-tests spectral_matcher [INFO] [stdout] test search_cli_runs_multiple_jobs ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.04s [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517", kill_on_drop: false }` [INFO] [stdout] f22976174346f4204825621911d8244568ef7cb77ba9276846814e2475829517