[INFO] fetching crate vcf-reformatter 0.3.0...
[INFO] testing vcf-reformatter-0.3.0 against master#caccb4d0368bd918ef6668af8e13834d07040417 for pr-146098-1
[INFO] extracting crate vcf-reformatter 0.3.0 into /workspace/builds/worker-6-tc1/source
[INFO] started tweaking crates.io crate vcf-reformatter 0.3.0
[INFO] removed 0 missing tests
[INFO] finished tweaking crates.io crate vcf-reformatter 0.3.0
[INFO] tweaked toml for crates.io crate vcf-reformatter 0.3.0 written to /workspace/builds/worker-6-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate vcf-reformatter 0.3.0 on toolchain caccb4d0368bd918ef6668af8e13834d07040417
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+caccb4d0368bd918ef6668af8e13834d07040417" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate vcf-reformatter 0.3.0 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" "+caccb4d0368bd918ef6668af8e13834d07040417" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+caccb4d0368bd918ef6668af8e13834d07040417" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 27f81407319cc808992706fef75f242102c4d2a71039b3e13325f5863710d9c8
[INFO] running `Command { std: "docker" "start" "-a" "27f81407319cc808992706fef75f242102c4d2a71039b3e13325f5863710d9c8", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "27f81407319cc808992706fef75f242102c4d2a71039b3e13325f5863710d9c8", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "27f81407319cc808992706fef75f242102c4d2a71039b3e13325f5863710d9c8", kill_on_drop: false }`
[INFO] [stdout] 27f81407319cc808992706fef75f242102c4d2a71039b3e13325f5863710d9c8
[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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+caccb4d0368bd918ef6668af8e13834d07040417" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 9250862e15f8fe7028f12339d17d1e8933384ba6e94f32285ea972783e95185c
[INFO] running `Command { std: "docker" "start" "-a" "9250862e15f8fe7028f12339d17d1e8933384ba6e94f32285ea972783e95185c", kill_on_drop: false }`
[INFO] [stderr]    Compiling crc32fast v1.4.2
[INFO] [stderr]    Compiling rustix v1.0.7
[INFO] [stderr]    Compiling regex-automata v0.4.9
[INFO] [stderr]    Compiling num_cpus v1.17.0
[INFO] [stderr]    Compiling clap_derive v4.5.41
[INFO] [stderr]    Compiling rayon v1.10.0
[INFO] [stderr]    Compiling flate2 v1.1.2
[INFO] [stderr]    Compiling tempfile v3.20.0
[INFO] [stderr]    Compiling clap v4.5.41
[INFO] [stderr]    Compiling regex v1.11.1
[INFO] [stderr]    Compiling vcf-reformatter v0.3.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 11.33s
[INFO] running `Command { std: "docker" "inspect" "9250862e15f8fe7028f12339d17d1e8933384ba6e94f32285ea972783e95185c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "9250862e15f8fe7028f12339d17d1e8933384ba6e94f32285ea972783e95185c", kill_on_drop: false }`
[INFO] [stdout] 9250862e15f8fe7028f12339d17d1e8933384ba6e94f32285ea972783e95185c
[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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+caccb4d0368bd918ef6668af8e13834d07040417" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] bf7cb2c47671535bd391485a86356638968f9e3e30032822ef32f8e6a51143f3
[INFO] running `Command { std: "docker" "start" "-a" "bf7cb2c47671535bd391485a86356638968f9e3e30032822ef32f8e6a51143f3", kill_on_drop: false }`
[INFO] [stderr]    Compiling vcf-reformatter v0.3.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: duplicated attribute
[INFO] [stdout]     --> tests/test.rs:1933:1
[INFO] [stdout]      |
[INFO] [stdout] 1933 | #[test]
[INFO] [stdout]      | ^^^^^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(duplicate_macro_attributes)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `reformat_vcf`
[INFO] [stdout]   --> tests/test.rs:12:5
[INFO] [stdout]    |
[INFO] [stdout] 12 |     reformat_vcf,
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::Cursor`
[INFO] [stdout]     --> tests/test.rs:2378:5
[INFO] [stdout]      |
[INFO] [stdout] 2378 | use std::io::Cursor;
[INFO] [stdout]      |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 2.94s
[INFO] running `Command { std: "docker" "inspect" "bf7cb2c47671535bd391485a86356638968f9e3e30032822ef32f8e6a51143f3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "bf7cb2c47671535bd391485a86356638968f9e3e30032822ef32f8e6a51143f3", kill_on_drop: false }`
[INFO] [stdout] bf7cb2c47671535bd391485a86356638968f9e3e30032822ef32f8e6a51143f3
[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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+caccb4d0368bd918ef6668af8e13834d07040417" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] de8572020dc2626585d2b5925827ef035bd653f0207e6b12e40314e443e113ed
[INFO] running `Command { std: "docker" "start" "-a" "de8572020dc2626585d2b5925827ef035bd653f0207e6b12e40314e443e113ed", kill_on_drop: false }`
[INFO] [stderr] warning: duplicated attribute
[INFO] [stderr]     --> tests/test.rs:1933:1
[INFO] [stderr]      |
[INFO] [stderr] 1933 | #[test]
[INFO] [stderr]      | ^^^^^^^
[INFO] [stderr]      |
[INFO] [stderr]      = note: `#[warn(duplicate_macro_attributes)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `reformat_vcf`
[INFO] [stderr]   --> tests/test.rs:12:5
[INFO] [stderr]    |
[INFO] [stderr] 12 |     reformat_vcf,
[INFO] [stderr]    |     ^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::io::Cursor`
[INFO] [stderr]     --> tests/test.rs:2378:5
[INFO] [stderr]      |
[INFO] [stderr] 2378 | use std::io::Cursor;
[INFO] [stderr]      |     ^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: `vcf-reformatter` (test "test") generated 3 warnings (run `cargo fix --test "test"` to apply 2 suggestions)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.12s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/vcf_reformatter-386cd5efafd18f2e)
[INFO] [stdout] 
[INFO] [stdout] running 2 tests
[INFO] [stdout] test extract_sample_info::tests::test_parse_format_and_samples ... ok
[INFO] [stdout] test extract_sample_info::tests::test_get_headers_for_samples ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 2 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/vcf_reformatter-7b1d440233a276e1)
[INFO] [stdout] 
[INFO] [stdout] running 2 tests
[INFO] [stdout] test extract_sample_info::tests::test_get_headers_for_samples ... ok
[INFO] [stdout] test extract_sample_info::tests::test_parse_format_and_samples ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 2 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/test.rs (/opt/rustwide/target/debug/deps/test-835e9bf6115a14cd)
[INFO] [stdout] 
[INFO] [stdout] running 77 tests
[INFO] [stdout] test test_complex_sample_names_header_generation ... ok
[INFO] [stdout] test test_edge_case_sample_names_with_multiple_underscores ... ok
[INFO] [stdout] test test_basic_vcf_processing ... ok
[INFO] [stdout] test test_extract_all_info_descriptions ... ok
[INFO] [stdout] test test_extract_csq_format_from_header ... ok
[INFO] [stdout] test test_complex_sample_names_value_extraction ... ok
[INFO] [stdout] test test_extract_csq_format_from_header_missing_csq ... ok
[INFO] [stdout] test test_empty_ann_field_handling ... ok
[INFO] [stdout] test test_extract_csq_regex_empty_csq ... ok
[INFO] [stdout] test test_extract_csq_regex ... ok
[INFO] [stdout] test test_extract_all_info_descriptions_no_info ... ok
[INFO] [stdout] test test_get_ann_impact_severity ... ok
[INFO] [stdout] test test_extract_csq_regex_too_few_fields ... ok
[INFO] [stdout] test test_extract_csq_format_from_header_no_format ... ok
[INFO] [stdout] test test_get_values_for_samples ... ok
[INFO] [stdout] test test_complex_sample_names_with_underscores ... ok
[INFO] [stdout] test test_maf_deletion_positions ... ok
[INFO] [stdout] test test_maf_chromosome_normalization ... ok
[INFO] [stdout] test test_maf_frameshift_classification ... ok
[INFO] [stdout] test test_maf_headers_completeness ... ok
[INFO] [stdout] test test_maf_depth_extraction ... ok
[INFO] [stdout] test test_maf_edge_cases ... ok
[INFO] [stdout] test test_maf_missing_annotations ... ok
[INFO] [stdout] test test_maf_intron_and_utr_variants ... ok
[INFO] [stdout] test test_maf_multi_allelic_conversion ... ok
[INFO] [stdout] test test_maf_multi_allelic_handling ... ok
[INFO] [stdout] test test_maf_multi_deletion_conversion ... ok
[INFO] [stdout] test test_extract_csq_regex_no_csq ... ok
[INFO] [stdout] test test_maf_file_write_integration ... ok
[INFO] [stdout] test test_maf_insertion_positions ... ok
[INFO] [stdout] test test_maf_snp_creation ... ok
[INFO] [stdout] test test_maf_tsv_line_format ... ok
[INFO] [stdout] test test_maf_vaf_calculation ... ok
[INFO] [stdout] test test_maf_real_world_data_simulation ... ok
[INFO] [stdout] test test_maf_vaf_calculation ... ok
[INFO] [stdout] test test_maf_variant_classification_mapping ... ok
[INFO] [stdout] test test_maf_vep_vs_snpeff_annotations ... ok
[INFO] [stdout] test test_parse_format_and_samples ... ok
[INFO] [stdout] test test_parse_format_and_samples_missing_fields ... ok
[INFO] [stdout] test test_parse_format_and_samples_no_format ... ok
[INFO] [stdout] test test_parse_info_field_empty ... ok
[INFO] [stdout] test test_parse_info_field_with_csq ... ok
[INFO] [stdout] test test_mixed_info_fields_with_ann ... ok
[INFO] [stdout] test test_parse_info_field_with_ann ... ok
[INFO] [stdout] test test_parse_info_field_no_annotations ... ok
[INFO] [stdout] test test_real_world_snpeff_header_extraction ... ok
[INFO] [stdout] test test_full_pipeline_with_snpeff_data ... ok
[INFO] [stdout] test test_snpeff_ann_impact_severity_ranking ... ok
[INFO] [stdout] test test_sanitize_field_name ... ok
[INFO] [stdout] test test_reformat_vcf_data_with_csq ... ok
[INFO] [stdout] test test_reformat_vcf_data_with_split_transcripts ... ok
[INFO] [stdout] test test_tsv_output_with_complex_sample_names ... ok
[INFO] [stdout] test test_snpeff_ann_parsing_basic ... ok
[INFO] [stdout] test test_vcf_record_with_complex_sample_names ... ok
[INFO] [stdout] test test_snpeff_ann_most_severe_selection ... ok
[INFO] [stdout] test test_snpeff_ann_multiple_transcripts_split_rows ... ok
[INFO] [stdout] test test_vcf_variant_invalid_position ... ok
[INFO] [stdout] test test_vcf_variant_missing_quality ... ok
[INFO] [stdout] test test_vcf_variant_parsing ... ok
[INFO] [stdout] test test_vcf_variant_with_id_and_samples ... ok
[INFO] [stdout] test test_vcf_with_empty_lines ... ok
[INFO] [stdout] test test_vcf_with_multiple_lines ... ok
[INFO] [stdout] test test_vep_and_snpeff_field_name_sanitization ... ok
[INFO] [stdout] test test_write_reformatted_vcf ... ok
[INFO] [stdout] test test_vcf_variant_too_few_fields ... ok
[INFO] [stdout] test test_reformat_vcf_data_with_most_severe ... ok
[INFO] [stdout] test test_reformat_vcf_data_with_header ... ok
[INFO] [stdout] test test_get_headers_for_samples ... ok
[INFO] [stdout] test test_maf_output ... ok
[INFO] [stdout] test test_chunked_error_handling ... ok
[INFO] [stdout] test test_chunk_boundary_integrity has been running for over 60 seconds
[INFO] [stdout] test test_chunked_streaming_basic has been running for over 60 seconds
[INFO] [stdout] test test_chunked_vs_regular_consistency has been running for over 60 seconds
[INFO] [stdout] test test_chunked_with_vep_annotations has been running for over 60 seconds
[INFO] [stdout] test test_large_dataset_streaming has been running for over 60 seconds
[INFO] [stdout] test test_parallel_processing has been running for over 60 seconds
[INFO] [stdout] test test_streaming_performance_benchmark has been running for over 60 seconds
[ERROR] error running command: no output for 300 seconds
[INFO] running `Command { std: "docker" "inspect" "de8572020dc2626585d2b5925827ef035bd653f0207e6b12e40314e443e113ed", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "de8572020dc2626585d2b5925827ef035bd653f0207e6b12e40314e443e113ed", kill_on_drop: false }`
[INFO] [stdout] de8572020dc2626585d2b5925827ef035bd653f0207e6b12e40314e443e113ed