[INFO] fetching crate gtf_splice_index 0.4.0...
[INFO] testing gtf_splice_index-0.4.0 against master#562dee4820c458d823175268e41601d4c060588a for pr-154210-1
[INFO] extracting crate gtf_splice_index 0.4.0 into /workspace/builds/worker-4-tc1/source
[INFO] started tweaking crates.io crate gtf_splice_index 0.4.0
[INFO] finished tweaking crates.io crate gtf_splice_index 0.4.0
[INFO] tweaked toml for crates.io crate gtf_splice_index 0.4.0 written to /workspace/builds/worker-4-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate gtf_splice_index 0.4.0 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 gtf_splice_index 0.4.0 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] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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] 160cf3a455f51bfbdf3d6a267901f70f116d063c4cc21c0bd3ff396e153ab108
[INFO] running `Command { std: "docker" "start" "-a" "160cf3a455f51bfbdf3d6a267901f70f116d063c4cc21c0bd3ff396e153ab108", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "160cf3a455f51bfbdf3d6a267901f70f116d063c4cc21c0bd3ff396e153ab108", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "160cf3a455f51bfbdf3d6a267901f70f116d063c4cc21c0bd3ff396e153ab108", kill_on_drop: false }`
[INFO] [stdout] 160cf3a455f51bfbdf3d6a267901f70f116d063c4cc21c0bd3ff396e153ab108
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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] d023c488f9905dadb18c280fa86c8a8f90210183eed2ed90f095b0c215d0d7e6
[INFO] running `Command { std: "docker" "start" "-a" "d023c488f9905dadb18c280fa86c8a8f90210183eed2ed90f095b0c215d0d7e6", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.182
[INFO] [stderr]    Compiling zstd-safe v7.2.4
[INFO] [stderr]    Compiling syn v2.0.116
[INFO] [stderr]    Compiling clap_builder v4.5.59
[INFO] [stderr]    Compiling flate2 v1.1.9
[INFO] [stderr]    Compiling jobserver v0.1.34
[INFO] [stderr]    Compiling cc v1.2.56
[INFO] [stderr]    Compiling zstd-sys v2.0.16+zstd.1.5.7
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling clap_derive v4.5.55
[INFO] [stderr]    Compiling clap v4.5.59
[INFO] [stderr]    Compiling serde v1.0.228
[INFO] [stderr]    Compiling bincode v1.3.3
[INFO] [stderr]    Compiling zstd v0.13.3
[INFO] [stderr]    Compiling gtf_splice_index v0.4.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `Strand`
[INFO] [stdout]  --> src/index.rs:9:43
[INFO] [stdout]   |
[INFO] [stdout] 9 | use crate::types::{RefBlock, SplicedRead, Strand};
[INFO] [stdout]   |                                           ^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `introns` and `overlaps` are never used
[INFO] [stdout]    --> src/model/transcript.rs:59:8
[INFO] [stdout]     |
[INFO] [stdout]  17 | impl Transcript {
[INFO] [stdout]     | --------------- associated items in this implementation
[INFO] [stdout] ...
[INFO] [stdout]  59 |     fn introns(&self) -> Vec<RefBlock> {
[INFO] [stdout]     |        ^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 120 |     fn overlaps(a0: u32, a1: u32, b0: u32, b1: u32) -> bool {
[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 22.56s
[INFO] running `Command { std: "docker" "inspect" "d023c488f9905dadb18c280fa86c8a8f90210183eed2ed90f095b0c215d0d7e6", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d023c488f9905dadb18c280fa86c8a8f90210183eed2ed90f095b0c215d0d7e6", kill_on_drop: false }`
[INFO] [stdout] d023c488f9905dadb18c280fa86c8a8f90210183eed2ed90f095b0c215d0d7e6
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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] f1468d02c991466dad63dea2c8902664d9766bccca9c2e4a50cf51dc931e68ca
[INFO] running `Command { std: "docker" "start" "-a" "f1468d02c991466dad63dea2c8902664d9766bccca9c2e4a50cf51dc931e68ca", kill_on_drop: false }`
[INFO] [stderr]    Compiling gtf_splice_index v0.4.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `Strand`
[INFO] [stdout]  --> src/index.rs:9:43
[INFO] [stdout]   |
[INFO] [stdout] 9 | use crate::types::{RefBlock, SplicedRead, Strand};
[INFO] [stdout]   |                                           ^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `introns` and `overlaps` are never used
[INFO] [stdout]    --> src/model/transcript.rs:59:8
[INFO] [stdout]     |
[INFO] [stdout]  17 | impl Transcript {
[INFO] [stdout]     | --------------- associated items in this implementation
[INFO] [stdout] ...
[INFO] [stdout]  59 |     fn introns(&self) -> Vec<RefBlock> {
[INFO] [stdout]     |        ^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 120 |     fn overlaps(a0: u32, a1: u32, b0: u32, b1: u32) -> bool {
[INFO] [stdout]     |        ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs`
[INFO] [stdout]     --> src/index.rs:1010:9
[INFO] [stdout]      |
[INFO] [stdout] 1010 |     use std::fs;
[INFO] [stdout]      |         ^^^^^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `introns` and `overlaps` are never used
[INFO] [stdout]    --> src/model/transcript.rs:59:8
[INFO] [stdout]     |
[INFO] [stdout]  17 | impl Transcript {
[INFO] [stdout]     | --------------- associated items in this implementation
[INFO] [stdout] ...
[INFO] [stdout]  59 |     fn introns(&self) -> Vec<RefBlock> {
[INFO] [stdout]     |        ^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 120 |     fn overlaps(a0: u32, a1: u32, b0: u32, b1: u32) -> bool {
[INFO] [stdout]     |        ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 2.43s
[INFO] running `Command { std: "docker" "inspect" "f1468d02c991466dad63dea2c8902664d9766bccca9c2e4a50cf51dc931e68ca", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f1468d02c991466dad63dea2c8902664d9766bccca9c2e4a50cf51dc931e68ca", kill_on_drop: false }`
[INFO] [stdout] f1468d02c991466dad63dea2c8902664d9766bccca9c2e4a50cf51dc931e68ca
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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] 8beb1b8762d3561198d1e82b31e74aaebded525a8b8e2d1b4d19388abb58e083
[INFO] running `Command { std: "docker" "start" "-a" "8beb1b8762d3561198d1e82b31e74aaebded525a8b8e2d1b4d19388abb58e083", kill_on_drop: false }`
[INFO] [stderr] warning: unused import: `Strand`
[INFO] [stderr]  --> src/index.rs:9:43
[INFO] [stderr]   |
[INFO] [stderr] 9 | use crate::types::{RefBlock, SplicedRead, Strand};
[INFO] [stderr]   |                                           ^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: associated items `introns` and `overlaps` are never used
[INFO] [stderr]    --> src/model/transcript.rs:59:8
[INFO] [stderr]     |
[INFO] [stderr]  17 | impl Transcript {
[INFO] [stderr]     | --------------- associated items in this implementation
[INFO] [stderr] ...
[INFO] [stderr]  59 |     fn introns(&self) -> Vec<RefBlock> {
[INFO] [stderr]     |        ^^^^^^^
[INFO] [stderr] ...
[INFO] [stderr] 120 |     fn overlaps(a0: u32, a1: u32, b0: u32, b1: u32) -> bool {
[INFO] [stderr]     |        ^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: `gtf_splice_index` (lib) generated 2 warnings (run `cargo fix --lib -p gtf_splice_index` to apply 1 suggestion)
[INFO] [stderr] warning: unused import: `std::fs`
[INFO] [stderr]     --> src/index.rs:1010:9
[INFO] [stderr]      |
[INFO] [stderr] 1010 |     use std::fs;
[INFO] [stderr]      |         ^^^^^^^
[INFO] [stderr]      |
[INFO] [stderr]      = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: `gtf_splice_index` (lib test) generated 2 warnings (1 duplicate) (run `cargo fix --lib -p gtf_splice_index --tests` to apply 1 suggestion)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.06s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/gtf_splice_index-37343e76c03f02e0)
[INFO] [stdout] 
[INFO] [stdout] running 28 tests
[INFO] [stdout] test annotation::builder::tests::builder_gtf_default_keys_builds_index ... ok
[INFO] [stdout] test annotation::builder::tests::builder_gff3_parent_linking_builds_index ... ok
[INFO] [stdout] test annotation::io::tests::parse_fails_on_invalid_strand ... ok
[INFO] [stdout] test annotation::io::tests::parse_fails_on_wrong_column_count ... ok
[INFO] [stdout] test annotation::io::tests::parse_gtf_line_ok ... ok
[INFO] [stdout] test annotation::io::tests::parse_fails_on_unbalanced_gtf_quotes ... ok
[INFO] [stdout] test annotation::builder::tests::builder_respects_exon_feature_types_filter ... ok
[INFO] [stdout] test index::tests::splice_index_internal_structure_is_consistent_and_deterministic ... ok
[INFO] [stdout] test model::gene::tests::contains_transcript_works_even_without_finalize ... ok
[INFO] [stdout] test model::gene::tests::add_and_finalize_sorts_and_dedups ... ok
[INFO] [stdout] test index::tests::competitive_match_transcripts_and_genes_choose_correct_winner ... ok
[INFO] [stdout] test annotation::io::tests::parse_gff3_line_ok ... ok
[INFO] [stdout] test model::gene::tests::transcripts_finalize_dedups ... ok
[INFO] [stdout] test model::transcript::tests::exact_chain_and_overhang_reported ... ok
[INFO] [stdout] test model::transcript::tests::exact_chain_with_sequenceing_errors ... ok
[INFO] [stdout] test model::transcript::tests::matchclass_nooverlap_same_chr_far_away ... ok
[INFO] [stdout] test model::transcript::tests::matchclass_junction_mismatch_skipping_middle_exon ... ok
[INFO] [stdout] test model::transcript::tests::matchclass_compatible_when_junctions_are_subset ... ok
[INFO] [stdout] test model::transcript::tests::transcript_names_dedup ... ok
[INFO] [stdout] test types::tests::spliced_read_finalize_sorts_and_merges ... ok
[INFO] [stdout] test types::tests::refblock_junctions ... ok
[INFO] [stdout] test index::tests::splice_index_save_load_roundtrip_preserves_internal_structure ... ok
[INFO] [stdout] test model::transcript::tests::matchclass_strand_mismatch_when_required ... ok
[INFO] [stdout] test annotation::io::tests::streaming_reader_skips_comments_and_blank_lines ... ok
[INFO] [stdout] test model::transcript::tests::matchclass_overhang_too_large ... ok
[INFO] [stdout] test model::gene::tests::names_are_deduped_and_primary_kept ... ok
[INFO] [stdout] test model::transcript::tests::require_exact_junction_chain_rejects_subset_as_junction_mismatch ... ok
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/gtf_splice_index-d6695509937ae676)
[INFO] [stdout] test model::transcript::tests::matchclass_intronic_due_to_intron_overlap ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 28 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] [stderr]    Doc-tests gtf_splice_index
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stdout] test src/index.rs - index::SpliceIndex::from_reader (line 453) ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stdout] all doctests ran in 0.74s; merged doctests compilation took 0.72s
[INFO] running `Command { std: "docker" "inspect" "8beb1b8762d3561198d1e82b31e74aaebded525a8b8e2d1b4d19388abb58e083", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8beb1b8762d3561198d1e82b31e74aaebded525a8b8e2d1b4d19388abb58e083", kill_on_drop: false }`
[INFO] [stdout] 8beb1b8762d3561198d1e82b31e74aaebded525a8b8e2d1b4d19388abb58e083