[INFO] fetching crate hpo 0.12.0... [INFO] testing hpo-0.12.0 against master#cdb45c87e2cd43495379f7e867e3cc15dcee9f93 for pr-145838-1 [INFO] extracting crate hpo 0.12.0 into /workspace/builds/worker-2-tc1/source [INFO] started tweaking crates.io crate hpo 0.12.0 [INFO] removed 0 missing examples [INFO] finished tweaking crates.io crate hpo 0.12.0 [INFO] tweaked toml for crates.io crate hpo 0.12.0 written to /workspace/builds/worker-2-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate hpo 0.12.0 on toolchain cdb45c87e2cd43495379f7e867e3cc15dcee9f93 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+cdb45c87e2cd43495379f7e867e3cc15dcee9f93" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate hpo 0.12.0 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" "+cdb45c87e2cd43495379f7e867e3cc15dcee9f93" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded simple_logger v4.3.3 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+cdb45c87e2cd43495379f7e867e3cc15dcee9f93" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] d827fb630185179e06fc078f0606588e5f89a1f4e702a5805c6469fd45e7695d [INFO] running `Command { std: "docker" "start" "-a" "d827fb630185179e06fc078f0606588e5f89a1f4e702a5805c6469fd45e7695d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "d827fb630185179e06fc078f0606588e5f89a1f4e702a5805c6469fd45e7695d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "d827fb630185179e06fc078f0606588e5f89a1f4e702a5805c6469fd45e7695d", kill_on_drop: false }` [INFO] [stdout] d827fb630185179e06fc078f0606588e5f89a1f4e702a5805c6469fd45e7695d [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+cdb45c87e2cd43495379f7e867e3cc15dcee9f93" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 52ee882544b6dd20951d622d21a08bfaba4aad46b9edd0c2c96cc8de8a0095fb [INFO] running `Command { std: "docker" "start" "-a" "52ee882544b6dd20951d622d21a08bfaba4aad46b9edd0c2c96cc8de8a0095fb", kill_on_drop: false }` [INFO] [stderr] Compiling thiserror-impl v2.0.11 [INFO] [stderr] Compiling thiserror v2.0.11 [INFO] [stderr] Compiling hpo v0.12.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unnecessary parentheses around `match` scrutinee expression [INFO] [stdout] --> src/parser/binary.rs:137:13 [INFO] [stdout] | [INFO] [stdout] 137 | (bytes.len() >= term_len), [INFO] [stdout] | ^ ^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 137 - (bytes.len() >= term_len), [INFO] [stdout] 137 + bytes.len() >= term_len, [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 3.80s [INFO] running `Command { std: "docker" "inspect" "52ee882544b6dd20951d622d21a08bfaba4aad46b9edd0c2c96cc8de8a0095fb", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "52ee882544b6dd20951d622d21a08bfaba4aad46b9edd0c2c96cc8de8a0095fb", kill_on_drop: false }` [INFO] [stdout] 52ee882544b6dd20951d622d21a08bfaba4aad46b9edd0c2c96cc8de8a0095fb [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+cdb45c87e2cd43495379f7e867e3cc15dcee9f93" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 7d46567c78989edfb4e69325830943cb6458217b4a8e498ee14290a608991aad [INFO] running `Command { std: "docker" "start" "-a" "7d46567c78989edfb4e69325830943cb6458217b4a8e498ee14290a608991aad", kill_on_drop: false }` [INFO] [stderr] Compiling indexmap v1.9.3 [INFO] [stderr] Compiling half v2.4.1 [INFO] [stderr] Compiling os_str_bytes v6.6.1 [INFO] [stderr] Compiling plotters-backend v0.3.7 [INFO] [stderr] Compiling ciborium-io v0.2.2 [INFO] [stderr] Compiling regex-automata v0.4.9 [INFO] [stderr] Compiling time-macros v0.2.19 [INFO] [stderr] Compiling itertools v0.10.5 [INFO] [stderr] Compiling textwrap v0.16.1 [INFO] [stderr] Compiling cast v0.3.0 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling colored v2.2.0 [INFO] [stderr] Compiling serde_json v1.0.139 [INFO] [stderr] Compiling rayon v1.10.0 [INFO] [stderr] Compiling log v0.4.26 [INFO] [stderr] Compiling oorandom v11.1.4 [INFO] [stderr] Compiling anes v0.1.6 [INFO] [stdout] warning: unnecessary parentheses around `match` scrutinee expression [INFO] [stdout] --> src/parser/binary.rs:137:13 [INFO] [stdout] | [INFO] [stdout] 137 | (bytes.len() >= term_len), [INFO] [stdout] | ^ ^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 137 - (bytes.len() >= term_len), [INFO] [stdout] 137 + bytes.len() >= term_len, [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling ciborium-ll v0.2.2 [INFO] [stderr] Compiling clap_lex v0.2.4 [INFO] [stderr] Compiling plotters-svg v0.3.7 [INFO] [stderr] Compiling ciborium v0.2.2 [INFO] [stderr] Compiling plotters v0.3.7 [INFO] [stderr] Compiling clap v3.2.25 [INFO] [stderr] Compiling tinytemplate v1.2.1 [INFO] [stderr] Compiling time v0.3.37 [INFO] [stderr] Compiling criterion-plot v0.5.0 [INFO] [stderr] Compiling regex v1.11.1 [INFO] [stderr] Compiling simple_logger v4.3.3 [INFO] [stderr] Compiling criterion v0.4.0 [INFO] [stderr] Compiling hpo v0.12.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unnecessary parentheses around `match` scrutinee expression [INFO] [stdout] --> src/parser/binary.rs:137:13 [INFO] [stdout] | [INFO] [stdout] 137 | (bytes.len() >= term_len), [INFO] [stdout] | ^ ^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 137 - (bytes.len() >= term_len), [INFO] [stdout] 137 + bytes.len() >= term_len, [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 21.05s [INFO] running `Command { std: "docker" "inspect" "7d46567c78989edfb4e69325830943cb6458217b4a8e498ee14290a608991aad", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "7d46567c78989edfb4e69325830943cb6458217b4a8e498ee14290a608991aad", kill_on_drop: false }` [INFO] [stdout] 7d46567c78989edfb4e69325830943cb6458217b4a8e498ee14290a608991aad [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+cdb45c87e2cd43495379f7e867e3cc15dcee9f93" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] afdd9480c56aade49f6c82a0796f51db568847f800acb0f580d35ea65be6e958 [INFO] running `Command { std: "docker" "start" "-a" "afdd9480c56aade49f6c82a0796f51db568847f800acb0f580d35ea65be6e958", kill_on_drop: false }` [INFO] [stderr] warning: unnecessary parentheses around `match` scrutinee expression [INFO] [stderr] --> src/parser/binary.rs:137:13 [INFO] [stderr] | [INFO] [stderr] 137 | (bytes.len() >= term_len), [INFO] [stderr] | ^ ^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] help: remove these parentheses [INFO] [stderr] | [INFO] [stderr] 137 - (bytes.len() >= term_len), [INFO] [stderr] 137 + bytes.len() >= term_len, [INFO] [stderr] | [INFO] [stderr] [INFO] [stderr] warning: `hpo` (lib) generated 1 warning (run `cargo fix --lib -p hpo` to apply 1 suggestion) [INFO] [stderr] warning: `hpo` (lib test) generated 1 warning (1 duplicate) [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-c1aa8057bd8ac04e) [INFO] [stdout] [INFO] [stdout] running 84 tests [INFO] [stdout] test annotations::gene::test::gene_to_and_from_binary ... 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_with_long_name ... ok [INFO] [stdout] test annotations::gene::test::gene_to_binary ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_to_and_from_binary ... ok [INFO] [stdout] test matrix::tests::test_column_index_iterator ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_with_wrong_length ... ok [INFO] [stdout] test matrix::tests::test_row_iterator_sums ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_with_non_utf8_name ... 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 parser::disease_to_hpo::test_omim_parsing::test_correct_orpha ... ok [INFO] [stdout] test matrix::tests::test_row_iterator ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_invalid_input ... 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_skip_comment ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_correct_omim ... 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_invalid_hpo_id ... 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_skip_orpha_not ... ok [INFO] [stdout] test matrix::tests::test_empty_row_iterator ... ok [INFO] [stdout] test parser::gene_to_hpo::test::test_remove_header_hpo_id ... ok [INFO] [stdout] test matrix::tests::test_row_index_iterator ... ok [INFO] [stdout] test parser::gene_to_hpo::test::test_remove_header_ncbi_gene ... 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_genes_to_phenotype::test_parse_missing_hpo ... ok [INFO] [stdout] test matrix::tests::test_column_iterator ... 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_correct_line_without_newline ... 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::test_remove_header_hashtag ... 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_phenotpye_to_genes::test_parse_correct_line_without_newline ... 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_missing_symbol ... 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_missing_hpo ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::min ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::test_fcache ... 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 matrix::tests::test_col_iterator_sums ... ok [INFO] [stdout] test parser::gene_to_hpo::test_phenotpye_to_genes::test_parse_empty_symbol ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::test_hypergeom_max ... ok [INFO] [stdout] test stats::test::iterate_frequencies ... ok [INFO] [stdout] test term::group::tests::test_bitand_2 ... ok [INFO] [stdout] test stats::test::iterate_counts ... ok [INFO] [stdout] test term::group::tests::test_bitand ... ok [INFO] [stdout] test term::group::tests::test_bitor_set4 ... ok [INFO] [stdout] test term::group::tests::test_hpogroup_iter ... ok [INFO] [stdout] test term::group::tests::test_bitor_set3 ... ok [INFO] [stdout] test term::group::tests::test_bitor_set2 ... ok [INFO] [stdout] test term::group::tests::test_bitor_set1 ... ok [INFO] [stdout] test ontology::test::add_parents_from_bytes ... ok [INFO] [stdout] test ontology::test::diseases_by_name ... ok [INFO] [stderr] error: test failed, to rerun pass `--lib` [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `/opt/rustwide/target/debug/deps/hpo-c1aa8057bd8ac04e` (signal: 9, SIGKILL: kill) [INFO] running `Command { std: "docker" "inspect" "afdd9480c56aade49f6c82a0796f51db568847f800acb0f580d35ea65be6e958", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "afdd9480c56aade49f6c82a0796f51db568847f800acb0f580d35ea65be6e958", kill_on_drop: false }` [INFO] [stdout] afdd9480c56aade49f6c82a0796f51db568847f800acb0f580d35ea65be6e958