[INFO] fetching crate kira-protein-pruner 0.1.1...
[INFO] testing kira-protein-pruner-0.1.1 against master#562dee4820c458d823175268e41601d4c060588a for pr-154210-1
[INFO] extracting crate kira-protein-pruner 0.1.1 into /workspace/builds/worker-0-tc1/source
[INFO] started tweaking crates.io crate kira-protein-pruner 0.1.1
[INFO] finished tweaking crates.io crate kira-protein-pruner 0.1.1
[INFO] tweaked toml for crates.io crate kira-protein-pruner 0.1.1 written to /workspace/builds/worker-0-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate kira-protein-pruner 0.1.1 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 kira-protein-pruner 0.1.1 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]     Updating crates.io index
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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] 86aa0607110150d0e4ece70ae503aee68ab20f8be60648835e5c97f2c929c778
[INFO] running `Command { std: "docker" "start" "-a" "86aa0607110150d0e4ece70ae503aee68ab20f8be60648835e5c97f2c929c778", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "86aa0607110150d0e4ece70ae503aee68ab20f8be60648835e5c97f2c929c778", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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] 0fb5bfd8e90dbeef784a2bc51a4373d7e2cd1e8681081827e6ba25614c4efb43
[INFO] running `Command { std: "docker" "start" "-a" "0fb5bfd8e90dbeef784a2bc51a4373d7e2cd1e8681081827e6ba25614c4efb43", kill_on_drop: false }`
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[INFO] [stderr]    Compiling icu_locale_core v2.1.1
[INFO] [stderr]    Compiling icu_collections v2.1.1
[INFO] [stderr]    Compiling bytemuck v1.25.0
[INFO] [stderr]    Compiling clap v4.5.57
[INFO] [stderr]    Compiling icu_provider v2.1.1
[INFO] [stderr]    Compiling icu_properties v2.1.2
[INFO] [stderr]    Compiling icu_normalizer v2.1.1
[INFO] [stderr]    Compiling serde v1.0.228
[INFO] [stderr]    Compiling idna_adapter v1.2.1
[INFO] [stderr]    Compiling idna v1.1.0
[INFO] [stderr]    Compiling flate2 v1.1.9
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[INFO] [stderr]    Compiling url v2.5.8
[INFO] [stderr]    Compiling kira_kv_engine v0.2.4
[INFO] [stdout] warning: value assigned to `graph_storage` is never read
[INFO] [stdout]    --> src/pipeline/interface/surface_analysis.rs:119:54
[INFO] [stdout]     |
[INFO] [stdout] 119 |     let mut graph_storage: Option<Vec<Vec<usize>>> = None;
[INFO] [stdout]     |                                                      ^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `compute_interface_stats` is never used
[INFO] [stdout]   --> src/pipeline/interface/surface_analysis.rs:86:15
[INFO] [stdout]    |
[INFO] [stdout] 86 | pub(crate) fn compute_interface_stats(
[INFO] [stdout]    |               ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 39s
[INFO] running `Command { std: "docker" "inspect" "0fb5bfd8e90dbeef784a2bc51a4373d7e2cd1e8681081827e6ba25614c4efb43", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "0fb5bfd8e90dbeef784a2bc51a4373d7e2cd1e8681081827e6ba25614c4efb43", kill_on_drop: false }`
[INFO] [stdout] 0fb5bfd8e90dbeef784a2bc51a4373d7e2cd1e8681081827e6ba25614c4efb43
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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] c6ab272aba0c18504c44d23a0a5d8f29925d93c6c5fd0f4e3b7168fdc0860aec
[INFO] running `Command { std: "docker" "start" "-a" "c6ab272aba0c18504c44d23a0a5d8f29925d93c6c5fd0f4e3b7168fdc0860aec", kill_on_drop: false }`
[INFO] [stdout] warning: value assigned to `graph_storage` is never read
[INFO] [stdout]    --> src/pipeline/interface/surface_analysis.rs:119:54
[INFO] [stdout]     |
[INFO] [stdout] 119 |     let mut graph_storage: Option<Vec<Vec<usize>>> = None;
[INFO] [stdout]     |                                                      ^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `compute_interface_stats` is never used
[INFO] [stdout]   --> src/pipeline/interface/surface_analysis.rs:86:15
[INFO] [stdout]    |
[INFO] [stdout] 86 | pub(crate) fn compute_interface_stats(
[INFO] [stdout]    |               ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]    Compiling kira-protein-pruner v0.1.1 (/opt/rustwide/workdir)
[INFO] [stdout] warning: value assigned to `graph_storage` is never read
[INFO] [stdout]    --> src/pipeline/interface/surface_analysis.rs:119:54
[INFO] [stdout]     |
[INFO] [stdout] 119 |     let mut graph_storage: Option<Vec<Vec<usize>>> = None;
[INFO] [stdout]     |                                                      ^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `compute_interface_stats` is never used
[INFO] [stdout]   --> src/pipeline/interface/surface_analysis.rs:86:15
[INFO] [stdout]    |
[INFO] [stdout] 86 | pub(crate) fn compute_interface_stats(
[INFO] [stdout]    |               ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: comparison is useless due to type limits
[INFO] [stdout]   --> src/pipeline/geometry/tests.rs:77:13
[INFO] [stdout]    |
[INFO] [stdout] 77 |     assert!(report.total_hbonds >= 0);
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_comparisons)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: comparison is useless due to type limits
[INFO] [stdout]   --> src/pipeline/geometry/tests.rs:87:13
[INFO] [stdout]    |
[INFO] [stdout] 87 |     assert!(report.unsatisfied_buried_polar_count >= 0);
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: comparison is useless due to type limits
[INFO] [stdout]   --> src/pipeline/structure_topology/tests.rs:44:13
[INFO] [stdout]    |
[INFO] [stdout] 44 |     assert!(report.short_helix_segments >= 0);
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: comparison is useless due to type limits
[INFO] [stdout]   --> src/pipeline/structure_topology/tests.rs:62:13
[INFO] [stdout]    |
[INFO] [stdout] 62 |     assert!(report.total_contacts >= 0);
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: comparison is useless due to type limits
[INFO] [stdout]   --> src/pipeline/structure_topology/tests.rs:71:13
[INFO] [stdout]    |
[INFO] [stdout] 71 |     assert!(report.component_count >= 0);
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 4.34s
[INFO] running `Command { std: "docker" "inspect" "c6ab272aba0c18504c44d23a0a5d8f29925d93c6c5fd0f4e3b7168fdc0860aec", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c6ab272aba0c18504c44d23a0a5d8f29925d93c6c5fd0f4e3b7168fdc0860aec", kill_on_drop: false }`
[INFO] [stdout] c6ab272aba0c18504c44d23a0a5d8f29925d93c6c5fd0f4e3b7168fdc0860aec
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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] 8dbacc0e92c8d453a806b024802fbae9e1634ad3af8be1f707e5b70352451d39
[INFO] running `Command { std: "docker" "start" "-a" "8dbacc0e92c8d453a806b024802fbae9e1634ad3af8be1f707e5b70352451d39", kill_on_drop: false }`
[INFO] [stderr] warning: value assigned to `graph_storage` is never read
[INFO] [stderr]    --> src/pipeline/interface/surface_analysis.rs:119:54
[INFO] [stderr]     |
[INFO] [stderr] 119 |     let mut graph_storage: Option<Vec<Vec<usize>>> = None;
[INFO] [stderr]     |                                                      ^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: function `compute_interface_stats` is never used
[INFO] [stderr]   --> src/pipeline/interface/surface_analysis.rs:86:15
[INFO] [stderr]    |
[INFO] [stderr] 86 | pub(crate) fn compute_interface_stats(
[INFO] [stderr]    |               ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: comparison is useless due to type limits
[INFO] [stderr]   --> src/pipeline/geometry/tests.rs:77:13
[INFO] [stderr]    |
[INFO] [stderr] 77 |     assert!(report.total_hbonds >= 0);
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(unused_comparisons)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: comparison is useless due to type limits
[INFO] [stderr]   --> src/pipeline/geometry/tests.rs:87:13
[INFO] [stderr]    |
[INFO] [stderr] 87 |     assert!(report.unsatisfied_buried_polar_count >= 0);
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: comparison is useless due to type limits
[INFO] [stderr]   --> src/pipeline/structure_topology/tests.rs:44:13
[INFO] [stderr]    |
[INFO] [stderr] 44 |     assert!(report.short_helix_segments >= 0);
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: comparison is useless due to type limits
[INFO] [stderr]   --> src/pipeline/structure_topology/tests.rs:62:13
[INFO] [stderr]    |
[INFO] [stderr] 62 |     assert!(report.total_contacts >= 0);
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: comparison is useless due to type limits
[INFO] [stderr]   --> src/pipeline/structure_topology/tests.rs:71:13
[INFO] [stderr]    |
[INFO] [stderr] 71 |     assert!(report.component_count >= 0);
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: `kira-protein-pruner` (lib) generated 2 warnings
[INFO] [stderr] warning: `kira-protein-pruner` (lib test) generated 7 warnings (2 duplicates)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.21s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/kira_protein_pruner-7e53c0827f4230c8)
[INFO] [stdout] 
[INFO] [stdout] running 23 tests
[INFO] [stdout] test core::short_report::tests::short_report_recommended_action_machine_code ... ok
[INFO] [stdout] test core::short_report::tests::short_report_basic_fields ... ok
[INFO] [stdout] test core::short_report::tests::short_report_recommended_action_no_free_text ... ok
[INFO] [stdout] test core::short_report::tests::short_report_reject_reason_root_cause ... ok
[INFO] [stdout] test core::short_report::tests::short_report_removes_secondary_when_topology_present ... ok
[INFO] [stdout] test pipeline::generative_output_sanity::tests::generative_sanity_passes_clean ... ok
[INFO] [stdout] test pipeline::geometry::tests::test_backbone_geometry_basic ... ok
[INFO] [stdout] test pipeline::geometry::tests::test_hbond_detects_pair ... ok
[INFO] [stdout] test pipeline::geometry::tests::test_packing_density_basic ... ok
[INFO] [stdout] test pipeline::generative_output_sanity::tests::generative_sanity_length_mismatch ... ok
[INFO] [stdout] test pipeline::geometry::tests::test_steric_clash_detects_overlap ... ok
[INFO] [stdout] test pipeline::geometry::tests::test_unsatisfied_polar_basic ... ok
[INFO] [stdout] test pipeline::interface::tests::interface_filters_basic ... ok
[INFO] [stdout] test pipeline::structure_confidence::tests::plddt_rejects_low_mean ... ok
[INFO] [stdout] test pipeline::structure_confidence::tests::plddt_passes_high_confidence ... ok
[INFO] [stdout] test pipeline::structure_topology::tests::test_contact_map_runs ... ok
[INFO] [stdout] test pipeline::structure_confidence::tests::pae_rejects_interface ... ok
[INFO] [stdout] test pipeline::structure_topology::tests::test_rg_runs ... ok
[INFO] [stdout] test pipeline::structure_topology::tests::test_secondary_composition_runs ... ok
[INFO] [stdout] test core::tests::tests::test_stability_score_range ... ok
[INFO] [stdout] test core::tests::tests::test_flexible_regions_counts ... ok
[INFO] [stdout] test pipeline::structure_topology::tests::test_fold_integrity_runs ... ok
[INFO] [stdout] test pipeline::structure_topology::tests::test_secondary_continuity_runs ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 23 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.02s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/bin/kira_protein_pruner.rs (/opt/rustwide/target/debug/deps/kira_protein_pruner-2a8c4a023dd0a951)
[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] [stderr]    Doc-tests kira_protein_pruner
[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" "8dbacc0e92c8d453a806b024802fbae9e1634ad3af8be1f707e5b70352451d39", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8dbacc0e92c8d453a806b024802fbae9e1634ad3af8be1f707e5b70352451d39", kill_on_drop: false }`
[INFO] [stdout] 8dbacc0e92c8d453a806b024802fbae9e1634ad3af8be1f707e5b70352451d39