[INFO] fetching crate hpo 0.12.0... [INFO] testing hpo-0.12.0 against master#562dee4820c458d823175268e41601d4c060588a for pr-154210-1 [INFO] extracting crate hpo 0.12.0 into /workspace/builds/worker-6-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-6-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate hpo 0.12.0 on toolchain 562dee4820c458d823175268e41601d4c060588a [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+562dee4820c458d823175268e41601d4c060588a" "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" "+562dee4820c458d823175268e41601d4c060588a" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Updating crates.io index [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded log v0.4.26 [INFO] [stderr] Downloaded once_cell v1.20.3 [INFO] [stderr] Downloaded simple_logger v4.3.3 [INFO] [stderr] Downloaded thiserror-impl v2.0.11 [INFO] [stderr] Downloaded textwrap v0.16.1 [INFO] [stderr] Downloaded serde_derive v1.0.218 [INFO] [stderr] Downloaded unicode-ident v1.0.17 [INFO] [stderr] Downloaded serde v1.0.218 [INFO] [stderr] Downloaded smallvec v1.14.0 [INFO] [stderr] Downloaded thiserror v2.0.11 [INFO] [stderr] Downloaded serde_json v1.0.139 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+562dee4820c458d823175268e41601d4c060588a" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 7a683a88df3199cbcadb27da88ceb92ef4ae1a6f8a1593ccb11c6636e2cfdbce [INFO] running `Command { std: "docker" "start" "-a" "7a683a88df3199cbcadb27da88ceb92ef4ae1a6f8a1593ccb11c6636e2cfdbce", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "7a683a88df3199cbcadb27da88ceb92ef4ae1a6f8a1593ccb11c6636e2cfdbce", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "7a683a88df3199cbcadb27da88ceb92ef4ae1a6f8a1593ccb11c6636e2cfdbce", kill_on_drop: false }` [INFO] [stdout] 7a683a88df3199cbcadb27da88ceb92ef4ae1a6f8a1593ccb11c6636e2cfdbce [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+562dee4820c458d823175268e41601d4c060588a" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 83dc00bc1dbab9003b1be21d001ea104b3fb64e919c4194135e6a8cd688a3d44 [INFO] running `Command { std: "docker" "start" "-a" "83dc00bc1dbab9003b1be21d001ea104b3fb64e919c4194135e6a8cd688a3d44", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.93 [INFO] [stderr] Compiling unicode-ident v1.0.17 [INFO] [stderr] Compiling thiserror v2.0.11 [INFO] [stderr] Compiling once_cell v1.20.3 [INFO] [stderr] Compiling smallvec v1.14.0 [INFO] [stderr] Compiling tracing-core v0.1.33 [INFO] [stderr] Compiling quote v1.0.38 [INFO] [stderr] Compiling syn v2.0.98 [INFO] [stderr] Compiling thiserror-impl v2.0.11 [INFO] [stderr] Compiling tracing-attributes v0.1.28 [INFO] [stderr] Compiling tracing v0.1.41 [INFO] [stderr] Compiling hpo v0.12.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 10.14s [INFO] running `Command { std: "docker" "inspect" "83dc00bc1dbab9003b1be21d001ea104b3fb64e919c4194135e6a8cd688a3d44", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "83dc00bc1dbab9003b1be21d001ea104b3fb64e919c4194135e6a8cd688a3d44", kill_on_drop: false }` [INFO] [stdout] 83dc00bc1dbab9003b1be21d001ea104b3fb64e919c4194135e6a8cd688a3d44 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+562dee4820c458d823175268e41601d4c060588a" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 6fc329ed4b8689abfbba7bae313136af188674cf12020a4bcd7b287af48c9a60 [INFO] running `Command { std: "docker" "start" "-a" "6fc329ed4b8689abfbba7bae313136af188674cf12020a4bcd7b287af48c9a60", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.4.0 [INFO] [stderr] Compiling serde v1.0.218 [INFO] [stderr] Compiling libc v0.2.169 [INFO] [stderr] Compiling serde_derive v1.0.218 [INFO] [stderr] Compiling itoa v1.0.14 [INFO] [stderr] Compiling either v1.13.0 [INFO] [stderr] Compiling serde_json v1.0.139 [INFO] [stderr] Compiling ciborium-io v0.2.2 [INFO] [stderr] Compiling hashbrown v0.12.3 [INFO] [stderr] Compiling os_str_bytes v6.6.1 [INFO] [stderr] Compiling half v2.4.1 [INFO] [stderr] Compiling regex-syntax v0.8.5 [INFO] [stderr] Compiling memchr v2.7.4 [INFO] [stderr] Compiling ryu v1.0.19 [INFO] [stderr] Compiling plotters-backend v0.3.7 [INFO] [stderr] Compiling time-macros v0.2.19 [INFO] [stderr] Compiling num_threads v0.1.7 [INFO] [stderr] Compiling textwrap v0.16.1 [INFO] [stderr] Compiling cast v0.3.0 [INFO] [stderr] Compiling walkdir v2.5.0 [INFO] [stderr] Compiling itertools v0.10.5 [INFO] [stderr] Compiling rayon v1.10.0 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling indexmap v1.9.3 [INFO] [stderr] Compiling plotters-svg v0.3.7 [INFO] [stderr] Compiling ciborium-ll v0.2.2 [INFO] [stderr] Compiling clap_lex v0.2.4 [INFO] [stderr] Compiling colored v2.2.0 [INFO] [stderr] Compiling oorandom v11.1.4 [INFO] [stderr] Compiling log v0.4.26 [INFO] [stderr] Compiling anes v0.1.6 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling time v0.3.37 [INFO] [stderr] Compiling criterion-plot v0.5.0 [INFO] [stderr] Compiling clap v3.2.25 [INFO] [stderr] Compiling plotters v0.3.7 [INFO] [stderr] Compiling regex-automata v0.4.9 [INFO] [stderr] Compiling simple_logger v4.3.3 [INFO] [stderr] Compiling regex v1.11.1 [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 v0.12.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 24.79s [INFO] running `Command { std: "docker" "inspect" "6fc329ed4b8689abfbba7bae313136af188674cf12020a4bcd7b287af48c9a60", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6fc329ed4b8689abfbba7bae313136af188674cf12020a4bcd7b287af48c9a60", kill_on_drop: false }` [INFO] [stdout] 6fc329ed4b8689abfbba7bae313136af188674cf12020a4bcd7b287af48c9a60 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+562dee4820c458d823175268e41601d4c060588a" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 454ae912eba16f3430c1e6a600ddd20fb5c433525a60e5f0ed9756ec823f87b9 [INFO] running `Command { std: "docker" "start" "-a" "454ae912eba16f3430c1e6a600ddd20fb5c433525a60e5f0ed9756ec823f87b9", kill_on_drop: false }` [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.13s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/hpo-6cb811edfd4a59cb) [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_long_name ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_to_and_from_binary ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_to_binary ... ok [INFO] [stdout] test annotations::gene::test::gene_with_wrong_length ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_with_non_utf8_name ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_with_long_name ... ok [INFO] [stdout] test matrix::tests::test_col_iterator_sums ... ok [INFO] [stdout] test annotations::omim_disease::test::disease_with_wrong_length ... 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_index_iterator ... ok [INFO] [stdout] test matrix::tests::test_row_iterator ... ok [INFO] [stdout] test matrix::tests::test_row_iterator_sums ... ok [INFO] [stdout] test matrix::tests::test_empty_row_iterator ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_correct_orpha ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_invalid_hpo_id ... 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::gene_to_hpo::test::test_remove_header_fails ... 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_skip_orpha_not ... 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_genes_to_phenotype::test_parse_missing_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_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_empty_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_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_genes_to_phenotype::test_parse_correct_line_with_newline ... ok [INFO] [stdout] test parser::disease_to_hpo::test_omim_parsing::test_invalid_omim_id ... ok [INFO] [stdout] test parser::gene_to_hpo::test::test_remove_header_hpo_id ... ok [INFO] [stdout] test annotations::gene::test::gene_to_binary ... 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_genes_to_phenotype::test_parse_missing_id ... ok [INFO] [stdout] test parser::gene_to_hpo::test::test_remove_header_ncbi_gene ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::test_hypergeom_cdf ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::test_hypergeom_max ... ok [INFO] [stdout] test stats::test::iterate_counts ... 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::min ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::test_fcache ... ok [INFO] [stdout] test stats::hypergeom::statrs::test::test_hypergeom_build ... 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-6cb811edfd4a59cb` (signal: 9, SIGKILL: kill) [INFO] running `Command { std: "docker" "inspect" "454ae912eba16f3430c1e6a600ddd20fb5c433525a60e5f0ed9756ec823f87b9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "454ae912eba16f3430c1e6a600ddd20fb5c433525a60e5f0ed9756ec823f87b9", kill_on_drop: false }` [INFO] [stdout] 454ae912eba16f3430c1e6a600ddd20fb5c433525a60e5f0ed9756ec823f87b9