[INFO] fetching crate hpo 0.11.0... [INFO] testing hpo-0.11.0 against beta-2024-12-08 for beta-1.84.0-4 [INFO] extracting crate hpo 0.11.0 into /workspace/builds/worker-5-tc2/source [INFO] validating manifest of crates.io crate hpo 0.11.0 on toolchain beta-2024-12-08 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2024-12-08" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate hpo 0.11.0 [INFO] removed 0 missing examples [INFO] finished tweaking crates.io crate hpo 0.11.0 [INFO] tweaked toml for crates.io crate hpo 0.11.0 written to /workspace/builds/worker-5-tc2/source/Cargo.toml [INFO] crate crates.io crate hpo 0.11.0 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" "+beta-2024-12-08" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:f3a9d4ad9d972b27faf3965f35b62e55ba32bbce8f20bc8fe909558a86702fde" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-12-08" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 3ca90035187a897a04767fac354e832d6201885ca30ae1ab4cb140a9be21eb15 [INFO] running `Command { std: "docker" "start" "-a" "3ca90035187a897a04767fac354e832d6201885ca30ae1ab4cb140a9be21eb15", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "3ca90035187a897a04767fac354e832d6201885ca30ae1ab4cb140a9be21eb15", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "3ca90035187a897a04767fac354e832d6201885ca30ae1ab4cb140a9be21eb15", kill_on_drop: false }` [INFO] [stdout] 3ca90035187a897a04767fac354e832d6201885ca30ae1ab4cb140a9be21eb15 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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:f3a9d4ad9d972b27faf3965f35b62e55ba32bbce8f20bc8fe909558a86702fde" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-12-08" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] cf14d35a463f5b1137d06212b9dd27fb249f0cf2a24a359c6bc5d006e4afd32e [INFO] running `Command { std: "docker" "start" "-a" "cf14d35a463f5b1137d06212b9dd27fb249f0cf2a24a359c6bc5d006e4afd32e", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.86 [INFO] [stderr] Compiling unicode-ident v1.0.12 [INFO] [stderr] Compiling thiserror v1.0.63 [INFO] [stderr] Compiling once_cell v1.19.0 [INFO] [stderr] Compiling pin-project-lite v0.2.14 [INFO] [stderr] Compiling tracing-core v0.1.32 [INFO] [stderr] Compiling quote v1.0.37 [INFO] [stderr] Compiling syn v2.0.77 [INFO] [stderr] Compiling tracing-attributes v0.1.27 [INFO] [stderr] Compiling thiserror-impl v1.0.63 [INFO] [stderr] Compiling tracing v0.1.40 [INFO] [stderr] Compiling hpo v0.11.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology/comparison.rs:391:44 [INFO] [stdout] | [INFO] [stdout] 331 | impl<'a> AnnotationDelta { [INFO] [stdout] | -- lifetime `'a` declared here [INFO] [stdout] ... [INFO] [stdout] 391 | pub fn added_terms(&'a self) -> Option<&Vec> { [INFO] [stdout] | ^ this elided lifetime gets resolved as `'a` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(elided_named_lifetimes)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology/comparison.rs:403:46 [INFO] [stdout] | [INFO] [stdout] 331 | impl<'a> AnnotationDelta { [INFO] [stdout] | -- lifetime `'a` declared here [INFO] [stdout] ... [INFO] [stdout] 403 | pub fn removed_terms(&'a self) -> Option<&Vec> { [INFO] [stdout] | ^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology.rs:651:71 [INFO] [stdout] | [INFO] [stdout] 651 | pub fn omim_diseases_by_name<'a>(&'a self, substring: &'a str) -> OmimDiseaseFilter { [INFO] [stdout] | -- lifetime `'a` declared here ^^^^^^^^^^^^^^^^^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology.rs:742:58 [INFO] [stdout] | [INFO] [stdout] 742 | pub fn compare<'a>(&'a self, other: &'a Ontology) -> Comparison { [INFO] [stdout] | -- lifetime `'a` declared here ^^^^^^^^^^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/stats/linkage.rs:16:40 [INFO] [stdout] | [INFO] [stdout] 15 | impl<'a> DistanceMatrix { [INFO] [stdout] | -- lifetime `'a` declared here [INFO] [stdout] 16 | fn iter(&'a self) -> hash_map::Iter<(usize, usize), f32> { [INFO] [stdout] | ^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 11.09s [INFO] running `Command { std: "docker" "inspect" "cf14d35a463f5b1137d06212b9dd27fb249f0cf2a24a359c6bc5d006e4afd32e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "cf14d35a463f5b1137d06212b9dd27fb249f0cf2a24a359c6bc5d006e4afd32e", kill_on_drop: false }` [INFO] [stdout] cf14d35a463f5b1137d06212b9dd27fb249f0cf2a24a359c6bc5d006e4afd32e [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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:f3a9d4ad9d972b27faf3965f35b62e55ba32bbce8f20bc8fe909558a86702fde" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-12-08" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 524c1ab0d109c28a8f53616031ce6f72accbce9ecadadad7bc8a81f34ac4d3c5 [INFO] running `Command { std: "docker" "start" "-a" "524c1ab0d109c28a8f53616031ce6f72accbce9ecadadad7bc8a81f34ac4d3c5", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.3.0 [INFO] [stderr] Compiling crossbeam-utils v0.8.20 [INFO] [stderr] Compiling serde v1.0.210 [INFO] [stderr] Compiling libc v0.2.158 [INFO] [stderr] Compiling itoa v1.0.11 [INFO] [stderr] Compiling serde_json v1.0.128 [INFO] [stderr] Compiling rayon-core v1.12.1 [INFO] [stderr] Compiling powerfmt v0.2.0 [INFO] [stderr] Compiling plotters-backend v0.3.7 [INFO] [stderr] Compiling ciborium-io v0.2.2 [INFO] [stderr] Compiling half v2.4.1 [INFO] [stderr] Compiling os_str_bytes v6.6.1 [INFO] [stderr] Compiling num-conv v0.1.0 [INFO] [stderr] Compiling ryu v1.0.18 [INFO] [stderr] Compiling hashbrown v0.12.3 [INFO] [stderr] Compiling serde_derive v1.0.210 [INFO] [stderr] Compiling regex-syntax v0.8.4 [INFO] [stderr] Compiling time-core v0.1.2 [INFO] [stderr] Compiling clap_lex v0.2.4 [INFO] [stderr] Compiling time-macros v0.2.18 [INFO] [stderr] Compiling deranged v0.3.11 [INFO] [stderr] Compiling cast v0.3.0 [INFO] [stderr] Compiling ciborium-ll v0.2.2 [INFO] [stderr] Compiling bitflags v1.3.2 [INFO] [stderr] Compiling textwrap v0.16.1 [INFO] [stderr] Compiling same-file v1.0.6 [INFO] [stderr] Compiling num_threads v0.1.7 [INFO] [stderr] Compiling plotters-svg v0.3.7 [INFO] [stderr] Compiling criterion-plot v0.5.0 [INFO] [stderr] Compiling colored v2.1.0 [INFO] [stderr] Compiling walkdir v2.5.0 [INFO] [stderr] Compiling oorandom v11.1.4 [INFO] [stderr] Compiling anes v0.1.6 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling indexmap v1.9.3 [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology/comparison.rs:391:44 [INFO] [stdout] | [INFO] [stdout] 331 | impl<'a> AnnotationDelta { [INFO] [stdout] | -- lifetime `'a` declared here [INFO] [stdout] ... [INFO] [stdout] 391 | pub fn added_terms(&'a self) -> Option<&Vec> { [INFO] [stdout] | ^ this elided lifetime gets resolved as `'a` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(elided_named_lifetimes)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology/comparison.rs:403:46 [INFO] [stdout] | [INFO] [stdout] 331 | impl<'a> AnnotationDelta { [INFO] [stdout] | -- lifetime `'a` declared here [INFO] [stdout] ... [INFO] [stdout] 403 | pub fn removed_terms(&'a self) -> Option<&Vec> { [INFO] [stdout] | ^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology.rs:651:71 [INFO] [stdout] | [INFO] [stdout] 651 | pub fn omim_diseases_by_name<'a>(&'a self, substring: &'a str) -> OmimDiseaseFilter { [INFO] [stdout] | -- lifetime `'a` declared here ^^^^^^^^^^^^^^^^^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology.rs:742:58 [INFO] [stdout] | [INFO] [stdout] 742 | pub fn compare<'a>(&'a self, other: &'a Ontology) -> Comparison { [INFO] [stdout] | -- lifetime `'a` declared here ^^^^^^^^^^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/stats/linkage.rs:16:40 [INFO] [stdout] | [INFO] [stdout] 15 | impl<'a> DistanceMatrix { [INFO] [stdout] | -- lifetime `'a` declared here [INFO] [stdout] 16 | fn iter(&'a self) -> hash_map::Iter<(usize, usize), f32> { [INFO] [stdout] | ^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling crossbeam-epoch v0.9.18 [INFO] [stderr] Compiling crossbeam-deque v0.8.5 [INFO] [stderr] Compiling clap v3.2.25 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling time v0.3.36 [INFO] [stderr] Compiling regex-automata v0.4.7 [INFO] [stderr] Compiling plotters v0.3.7 [INFO] [stderr] Compiling rayon v1.10.0 [INFO] [stderr] Compiling simple_logger v4.3.3 [INFO] [stderr] Compiling regex v1.10.6 [INFO] [stderr] Compiling ciborium v0.2.2 [INFO] [stderr] Compiling tinytemplate v1.2.1 [INFO] [stderr] Compiling criterion v0.4.0 [INFO] [stderr] Compiling hpo v0.11.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology/comparison.rs:391:44 [INFO] [stdout] | [INFO] [stdout] 331 | impl<'a> AnnotationDelta { [INFO] [stdout] | -- lifetime `'a` declared here [INFO] [stdout] ... [INFO] [stdout] 391 | pub fn added_terms(&'a self) -> Option<&Vec> { [INFO] [stdout] | ^ this elided lifetime gets resolved as `'a` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(elided_named_lifetimes)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology/comparison.rs:403:46 [INFO] [stdout] | [INFO] [stdout] 331 | impl<'a> AnnotationDelta { [INFO] [stdout] | -- lifetime `'a` declared here [INFO] [stdout] ... [INFO] [stdout] 403 | pub fn removed_terms(&'a self) -> Option<&Vec> { [INFO] [stdout] | ^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology.rs:651:71 [INFO] [stdout] | [INFO] [stdout] 651 | pub fn omim_diseases_by_name<'a>(&'a self, substring: &'a str) -> OmimDiseaseFilter { [INFO] [stdout] | -- lifetime `'a` declared here ^^^^^^^^^^^^^^^^^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/ontology.rs:742:58 [INFO] [stdout] | [INFO] [stdout] 742 | pub fn compare<'a>(&'a self, other: &'a Ontology) -> Comparison { [INFO] [stdout] | -- lifetime `'a` declared here ^^^^^^^^^^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: elided lifetime has a name [INFO] [stdout] --> src/stats/linkage.rs:16:40 [INFO] [stdout] | [INFO] [stdout] 15 | impl<'a> DistanceMatrix { [INFO] [stdout] | -- lifetime `'a` declared here [INFO] [stdout] 16 | fn iter(&'a self) -> hash_map::Iter<(usize, usize), f32> { [INFO] [stdout] | ^ this elided lifetime gets resolved as `'a` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 29.39s [INFO] running `Command { std: "docker" "inspect" "524c1ab0d109c28a8f53616031ce6f72accbce9ecadadad7bc8a81f34ac4d3c5", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "524c1ab0d109c28a8f53616031ce6f72accbce9ecadadad7bc8a81f34ac4d3c5", kill_on_drop: false }` [INFO] [stdout] 524c1ab0d109c28a8f53616031ce6f72accbce9ecadadad7bc8a81f34ac4d3c5 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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:f3a9d4ad9d972b27faf3965f35b62e55ba32bbce8f20bc8fe909558a86702fde" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-12-08" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 6ffb061807c24db5eb204ebf51eb9b72e9f4f9f0edfd764aea54ebb1b208c07f [INFO] running `Command { std: "docker" "start" "-a" "6ffb061807c24db5eb204ebf51eb9b72e9f4f9f0edfd764aea54ebb1b208c07f", kill_on_drop: false }` [INFO] [stderr] warning: elided lifetime has a name [INFO] [stderr] --> src/ontology/comparison.rs:391:44 [INFO] [stderr] | [INFO] [stderr] 331 | impl<'a> AnnotationDelta { [INFO] [stderr] | -- lifetime `'a` declared here [INFO] [stderr] ... [INFO] [stderr] 391 | pub fn added_terms(&'a self) -> Option<&Vec> { [INFO] [stderr] | ^ this elided lifetime gets resolved as `'a` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(elided_named_lifetimes)]` on by default [INFO] [stderr] [INFO] [stderr] warning: elided lifetime has a name [INFO] [stderr] --> src/ontology/comparison.rs:403:46 [INFO] [stderr] | [INFO] [stderr] 331 | impl<'a> AnnotationDelta { [INFO] [stderr] | -- lifetime `'a` declared here [INFO] [stderr] ... [INFO] [stderr] 403 | pub fn removed_terms(&'a self) -> Option<&Vec> { [INFO] [stderr] | ^ this elided lifetime gets resolved as `'a` [INFO] [stderr] [INFO] [stderr] warning: elided lifetime has a name [INFO] [stderr] --> src/ontology.rs:651:71 [INFO] [stderr] | [INFO] [stderr] 651 | pub fn omim_diseases_by_name<'a>(&'a self, substring: &'a str) -> OmimDiseaseFilter { [INFO] [stderr] | -- lifetime `'a` declared here ^^^^^^^^^^^^^^^^^ this elided lifetime gets resolved as `'a` [INFO] [stderr] [INFO] [stderr] warning: elided lifetime has a name [INFO] [stderr] --> src/ontology.rs:742:58 [INFO] [stderr] | [INFO] [stderr] 742 | pub fn compare<'a>(&'a self, other: &'a Ontology) -> Comparison { [INFO] [stderr] | -- lifetime `'a` declared here ^^^^^^^^^^ this elided lifetime gets resolved as `'a` [INFO] [stderr] [INFO] [stderr] warning: elided lifetime has a name [INFO] [stderr] --> src/stats/linkage.rs:16:40 [INFO] [stderr] | [INFO] [stderr] 15 | impl<'a> DistanceMatrix { [INFO] [stderr] | -- lifetime `'a` declared here [INFO] [stderr] 16 | fn iter(&'a self) -> hash_map::Iter<(usize, usize), f32> { [INFO] [stderr] | ^ this elided lifetime gets resolved as `'a` [INFO] [stderr] [INFO] [stderr] warning: `hpo` (lib) generated 5 warnings [INFO] [stderr] warning: `hpo` (lib test) generated 5 warnings (5 duplicates) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.12s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/hpo-2870dfb63ba7d619) [INFO] [stdout] [INFO] [stdout] running 84 tests [INFO] [stdout] test annotations::gene::test::gene_to_binary ... ok [INFO] [stdout] test annotations::gene::test::gene_with_long_name ... ok [INFO] [stdout] test annotations::gene::test::gene_with_non_utf8_name ... ok [INFO] [stdout] test annotations::gene::test::gene_with_wrong_length ... ok [INFO] [stdout] test annotations::gene::test::gene_to_and_from_binary ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_to_binary ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_with_long_name ... ok [INFO] [stdout] test matrix::tests::test_column_index_iterator ... ok [INFO] [stdout] test matrix::tests::test_column_iterator ... ok [INFO] [stdout] test matrix::tests::test_row_iterator ... ok [INFO] [stdout] test matrix::tests::test_row_iterator_sums ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_with_wrong_length ... ok [INFO] [stdout] test matrix::tests::test_empty_row_iterator ... ok [INFO] [stdout] test matrix::tests::test_row_index_iterator ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_invalid_hpo_id ... ok [INFO] [stdout] test matrix::tests::test_col_iterator_sums ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_invalid_omim_id ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_correct_omim ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_to_and_from_binary ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_correct_orpha ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_with_non_utf8_name ... ok [INFO] [stdout] test parser::gene_to_hpo::test::test_remove_header_fails ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_invalid_input ... ok [INFO] [stdout] test parser::gene_to_hpo::test::test_remove_header_hashtag ... ok [INFO] [stdout] test parser::gene_to_hpo::test::test_remove_header_ncbi_gene ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_skip_comment ... ok [INFO] [stdout] test parser::gene_to_hpo::test_genes_to_phenotype::test_parse_invalid_hpo ... ok [INFO] [stdout] test parser::gene_to_hpo::test_genes_to_phenotype::test_parse_missing_hpo ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_skip_not ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_skip_orpha_not ... ok [INFO] [stdout] test parser::gene_to_hpo::test_genes_to_phenotype::test_parse_correct_line_with_newline ... ok [INFO] [stdout] test parser::gene_to_hpo::test::test_remove_header_hpo_id ... ok [INFO] [stdout] test parser::gene_to_hpo::test_phenotpye_to_genes::test_parse_correct_line_with_newline ... ok [INFO] [stdout] test parser::gene_to_hpo::test_genes_to_phenotype::test_parse_missing_id ... ok [INFO] [stdout] test parser::gene_to_hpo::test_genes_to_phenotype::test_parse_missing_symbol ... ok [INFO] [stdout] test parser::gene_to_hpo::test_phenotpye_to_genes::test_parse_invalid_hpo ... ok [INFO] [stdout] test parser::gene_to_hpo::test_genes_to_phenotype::test_parse_correct_line_without_newline ... ok [INFO] [stdout] test parser::gene_to_hpo::test_phenotpye_to_genes::test_parse_missing_hpo ... ok [INFO] [stdout] test parser::gene_to_hpo::test_phenotpye_to_genes::test_parse_missing_id ... ok [INFO] [stdout] test parser::gene_to_hpo::test_phenotpye_to_genes::test_parse_correct_line_without_newline ... ok [INFO] [stdout] test parser::gene_to_hpo::test_phenotpye_to_genes::test_parse_empty_symbol ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::min ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::test_hypergeom_build ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::test_hypergeom_cdf ... ok [INFO] [stdout] test stats::test::iterate_frequencies ... ok [INFO] [stdout] test term::group::tests::test_bitand ... ok [INFO] [stdout] test term::group::tests::test_bitand_2 ... ok [INFO] [stdout] test term::group::tests::test_bitor_set1 ... ok [INFO] [stdout] test term::group::tests::test_bitor_set2 ... ok [INFO] [stdout] test term::group::tests::test_bitor_set3 ... ok [INFO] [stdout] test term::group::tests::test_bitor_set4 ... ok [INFO] [stdout] test term::group::tests::test_hpogroup_iter ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::test_fcache ... ok [INFO] [stdout] test stats::test::iterate_counts ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::test_hypergeom_max ... ok [INFO] [stdout] test term::hpoterm::test_categories::test_categories_is_self ... ok [INFO] [stdout] test set::test::test ... ok [INFO] [stdout] test ontology::test::diseases_by_name ... ok [INFO] [stdout] test term::hpoterm::test_categories::test_modifier_is_self ... ok [INFO] [stdout] test ontology::test::graphiv ... ok [INFO] [stdout] test term::internal::test::from_bytes ... ok [INFO] [stdout] test term::internal::test::from_multiple_bytes ... ok [INFO] [stdout] test term::internal::test::to_bytes ... ok [INFO] [stdout] test utils::test::combinations ... ok [INFO] [stdout] test utils::test::combinations_empty ... ok [INFO] [stdout] test ontology::test::add_parents_from_bytes ... ok [INFO] [stdout] test utils::test::combinations_single ... ok [INFO] [stdout] test utils::test::combinations_with_none ... ok [INFO] [stdout] test utils::test::combinations_two ... ok [INFO] [stdout] test utils::test::last_row ... ok [INFO] [stdout] test ontology::test::add_terms_from_bytes ... ok [INFO] [stdout] test term::hpoterm::test_path_to_term::normal ... ok [INFO] [stdout] test parser::hp_obo::test::split_terms ... ok [INFO] [stdout] test term::hpoterm::test_categories::test_categories ... ok [INFO] [stdout] test term::hpoterm::test_categories::test_modifier ... ok [INFO] [stdout] test ontology::test::check_v2_parsing ... ok [INFO] [stdout] test term::hpoterm::test_path_to_term::child_term ... ok [INFO] [stdout] test term::hpoterm::test_path_to_term::parent_term ... ok [INFO] [stdout] test ontology::test::parse_hpo_version ... ok [INFO] [stdout] test set::test::test_obsolete ... ok [INFO] [stdout] test term::hpoterm::test_path_to_term::same_term ... ok [INFO] [stdout] test set::test::test_replace_obsolete ... ok [INFO] [stdout] test set::test::test_with_replaced_obsolete ... ok [INFO] [stdout] test ontology::test::compare_v1_v2 ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 84 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 4.10s [INFO] [stdout] [INFO] [stderr] Doc-tests hpo [INFO] [stdout] [INFO] [stdout] running 141 tests [INFO] [stdout] test src/matrix.rs - matrix (line 14) - compile ... ok [INFO] [stdout] test src/lib.rs - (line 143) ... ok [INFO] [stdout] test src/lib.rs - (line 163) ... ok [INFO] [stdout] test src/matrix.rs - matrix::Matrix<'a,T>::dim (line 100) ... ok [INFO] [stdout] test src/lib.rs - (line 113) ... ok [INFO] [stdout] test src/annotations/disease.rs - annotations::disease::Disease::from_bytes (line 108) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology (line 111) - compile ... ok [INFO] [stdout] test src/annotations/gene.rs - annotations::gene::Gene::try_from (line 219) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology (line 85) - compile ... ok [INFO] [stdout] test src/matrix.rs - matrix::Matrix<'a,T>::len (line 74) ... ok [INFO] [stdout] test src/matrix.rs - matrix::Matrix<'a,T>::cols (line 138) ... ok [INFO] [stdout] test src/lib.rs - (line 59) ... ok [INFO] [stdout] test src/matrix.rs - matrix::Matrix<'a,T>::new (line 61) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::from_standard (line 260) - compile ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::from_standard_transitive (line 312) - compile ... ok [INFO] [stdout] test src/annotations/gene.rs - annotations::gene::Gene::as_bytes (line 142) ... ok [INFO] [stdout] test src/matrix.rs - matrix::Matrix<'a,T>::is_empty (line 87) ... ok [INFO] [stdout] test src/annotations/disease.rs - annotations::disease::Disease::as_bytes (line 52) ... ok [INFO] [stdout] test src/annotations/orpha_disease.rs - annotations::orpha_disease::OrphaDisease::try_from (line 123) ... ok [INFO] [stdout] test src/matrix.rs - matrix::Matrix<'a,T>::rows (line 113) ... ok [INFO] [stdout] test src/annotations/omim_disease.rs - annotations::omim_disease::OmimDisease::as_bytes (line 115) ... ok [INFO] [stdout] test src/annotations/omim_disease.rs - annotations::omim_disease::OmimDisease::try_from (line 191) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::categories (line 803) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::from_binary (line 360) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::is_empty (line 514) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::hpo (line 529) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::from_bytes (line 423) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::as_bytes (line 837) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::gene_by_name (line 567) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::iter (line 750) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::genes (line 586) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::gene (line 546) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::hpos (line 782) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::modifier (line 1110) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology (line 37) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::len (line 501) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::omim_disease (line 603) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::hpos (line 769) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::omim_diseases (line 621) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::compare (line 727) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::omim_diseases_by_name (line 641) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::omim_disease_by_name (line 662) ... ok [INFO] [stdout] test src/ontology/builder.rs - ontology::builder::Builder::add_parent (line 237) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::orpha_disease (line 682) ... ok [INFO] [stdout] test src/ontology/builder.rs - ontology::builder::Builder (line 86) ... ok [INFO] [stdout] test src/ontology/builder.rs - ontology::builder::Builder::calculate_information_content (line 609) ... ok [INFO] [stdout] test src/ontology/builder.rs - ontology::builder::Builder::connect_all_terms (line 345) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::orpha_diseases (line 699) ... ok [INFO] [stdout] test src/ontology/builder.rs - ontology::builder::Builder::annotate_gene (line 433) ... ok [INFO] [stdout] test src/ontology/comparison.rs - ontology::comparison (line 5) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::information_content (line 607) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::child_nodes (line 101) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::categories (line 557) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::contains (line 721) ... ok [INFO] [stdout] test src/ontology/builder.rs - ontology::builder::Builder::annotate_orpha_disease (line 548) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet (line 29) ... ok [INFO] [stdout] test src/ontology/builder.rs - ontology::builder::Builder::new_term (line 189) ... ok [INFO] [stdout] test src/ontology/builder.rs - ontology::builder::Builder::annotate_omim_disease (line 490) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::gene_ids (line 461) ... ok [INFO] [stdout] test src/ontology.rs - ontology::Ontology::sub_ontology (line 903) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::is_empty (line 165) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::remove_modifier (line 184) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::remove_obsolete (line 262) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::with_replaced_obsolete (line 363) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::len (line 142) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::iter (line 693) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::orpha_disease_ids (line 527) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::replace_obsolete (line 417) ... ok [INFO] [stdout] test src/similarity.rs - similarity::Builtins::new (line 480) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::new (line 75) ... ok [INFO] [stdout] test src/similarity/defaults.rs - similarity::defaults::Jc::new (line 172) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::omim_disease_ids (line 494) ... ok [INFO] [stdout] test src/similarity/defaults.rs - similarity::defaults::GraphIc::new (line 29) ... ok [INFO] [stdout] test src/similarity.rs - similarity::GroupSimilarity::new (line 368) ... ok [INFO] [stdout] test src/similarity/defaults.rs - similarity::defaults::InformationCoefficient::new (line 256) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::similarity (line 646) ... ok [INFO] [stdout] test src/similarity/defaults.rs - similarity::defaults::Distance::new (line 288) ... ok [INFO] [stdout] test src/similarity/defaults.rs - similarity::defaults::Resnik::new (line 82) ... ok [INFO] [stdout] test src/similarity/defaults.rs - similarity::defaults::Lin::new (line 118) ... ok [INFO] [stdout] test src/similarity.rs - similarity (line 31) ... ok [INFO] [stdout] test src/similarity.rs - similarity (line 11) ... ok [INFO] [stdout] test src/similarity.rs - similarity::GroupSimilarity (line 320) ... ok [INFO] [stdout] test src/similarity/defaults.rs - similarity::defaults::Relevance::new (line 219) ... ok [INFO] [stdout] test src/similarity/defaults.rs - similarity::defaults::Mutation::new (line 325) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::without_modifier (line 214) ... ok [INFO] [stdout] test src/similarity.rs - similarity::GroupSimilarity (line 278) ... ok [INFO] [stdout] test src/set.rs - set::HpoSet<'a>::without_obsolete (line 309) ... ok [INFO] [stdout] test src/similarity.rs - similarity::Builtins (line 417) ... ok [INFO] [stdout] test src/stats/linkage.rs - stats::linkage::Linkage (line 59) ... ok [INFO] [stdout] test src/stats/linkage.rs - stats::linkage::Linkage<'a>::indicies (line 281) ... ok [INFO] [stdout] test src/stats/hypergeom.rs - stats::hypergeom (line 9) ... ok [INFO] [stdout] test src/stats/hypergeom.rs - stats::hypergeom (line 45) ... ok [INFO] [stdout] test src/similarity.rs - similarity::Similarity (line 74) ... ok [INFO] [stdout] test src/stats/hypergeom/disease.rs - stats::hypergeom::disease::omim_disease_enrichment (line 12) ... ok [INFO] [stdout] test src/stats/hypergeom/gene.rs - stats::hypergeom::gene::gene_enrichment (line 12) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::all_common_ancestors (line 485) ... ok [INFO] [stdout] test src/stats/linkage.rs - stats::linkage::Linkage<'a>::union (line 113) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::all_common_ancestors (line 465) ... ok [INFO] [stdout] test src/stats/hypergeom/disease.rs - stats::hypergeom::disease::orpha_disease_enrichment (line 45) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::all_common_ancestor_ids (line 270) ... ok [INFO] [stdout] test src/stats/linkage.rs - stats::linkage::Linkage<'a>::single (line 166) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::all_union_ancestor_ids (line 379) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::all_parents (line 185) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::all_common_ancestor_ids (line 251) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::child_of (line 847) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::all_parent_ids (line 169) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::all_union_ancestor_ids (line 360) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::all_union_ancestors (line 593) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::all_union_ancestors (line 573) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::categories (line 1083) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::distance_to_term (line 927) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::children (line 220) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::children_ids (line 204) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::distance_to_ancestor (line 814) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::common_ancestors (line 515) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::gene_ids (line 687) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::common_ancestors (line 535) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::common_ancestor_ids (line 323) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::id (line 100) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::common_ancestor_ids (line 304) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::name (line 118) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::information_content (line 774) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::genes (line 669) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::is_modifier (line 1052) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::omim_diseases (line 703) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::omim_disease_ids (line 722) ... ok [INFO] [stdout] test src/utils.rs - utils::Combinations (line 7) - compile ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::orpha_disease_ids (line 757) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::orpha_diseases (line 738) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::similarity_score (line 793) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::path_to_term (line 955) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::path_to_ancestor (line 885) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::parent_ids (line 134) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::union_ancestor_ids (line 408) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::parents (line 150) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::parent_of (line 866) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::try_new (line 55) ... ok [INFO] [stdout] test src/term/hpotermid.rs - term::hpotermid::HpoTermId::from_u32 (line 37) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::union_ancestor_ids (line 427) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::union_ancestors (line 643) ... ok [INFO] [stdout] test src/term/hpoterm.rs - term::hpoterm::HpoTerm<'a>::union_ancestors (line 623) ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 141 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 40.49s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "6ffb061807c24db5eb204ebf51eb9b72e9f4f9f0edfd764aea54ebb1b208c07f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6ffb061807c24db5eb204ebf51eb9b72e9f4f9f0edfd764aea54ebb1b208c07f", kill_on_drop: false }` [INFO] [stdout] 6ffb061807c24db5eb204ebf51eb9b72e9f4f9f0edfd764aea54ebb1b208c07f