[INFO] fetching crate vareffect-cli 0.1.3...
[INFO] testing vareffect-cli-0.1.3 against master#ec6f9a5b4413f74386267ef8efc93712c2ce6db6 for pr-155739-1
[INFO] extracting crate vareffect-cli 0.1.3 into /workspace/builds/worker-3-tc1/source
[INFO] started tweaking crates.io crate vareffect-cli 0.1.3
[INFO] finished tweaking crates.io crate vareffect-cli 0.1.3
[INFO] tweaked toml for crates.io crate vareffect-cli 0.1.3 written to /workspace/builds/worker-3-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate vareffect-cli 0.1.3 on toolchain ec6f9a5b4413f74386267ef8efc93712c2ce6db6
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate vareffect-cli 0.1.3 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" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded sha2 v0.11.0
[INFO] [stderr]   Downloaded coitrees v0.4.0
[INFO] [stderr]   Downloaded vareffect v0.1.3
[INFO] [stderr]   Downloaded rustls v0.23.39
[INFO] [stderr]   Downloaded unit-prefix v0.5.2
[INFO] [stderr]   Downloaded libredox v0.1.16
[INFO] [stderr]   Downloaded clap_derive v4.6.1
[INFO] [stderr]   Downloaded indicatif v0.18.4
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 9f5649cf86db5a77628c915748141d792164f7adcb84cd2be0e19e47a550194f
[INFO] running `Command { std: "docker" "start" "-a" "9f5649cf86db5a77628c915748141d792164f7adcb84cd2be0e19e47a550194f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "9f5649cf86db5a77628c915748141d792164f7adcb84cd2be0e19e47a550194f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "9f5649cf86db5a77628c915748141d792164f7adcb84cd2be0e19e47a550194f", kill_on_drop: false }`
[INFO] [stdout] 9f5649cf86db5a77628c915748141d792164f7adcb84cd2be0e19e47a550194f
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] c27e19b33445fa4b1d7847335021b13827767462c2399ea13bb17a25f71b7821
[INFO] running `Command { std: "docker" "start" "-a" "c27e19b33445fa4b1d7847335021b13827767462c2399ea13bb17a25f71b7821", kill_on_drop: false }`
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[INFO] [stderr]    Compiling vareffect-cli v0.1.3 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 25s
[INFO] running `Command { std: "docker" "inspect" "c27e19b33445fa4b1d7847335021b13827767462c2399ea13bb17a25f71b7821", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c27e19b33445fa4b1d7847335021b13827767462c2399ea13bb17a25f71b7821", kill_on_drop: false }`
[INFO] [stdout] c27e19b33445fa4b1d7847335021b13827767462c2399ea13bb17a25f71b7821
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 2b2b2ce005d4d5560541a484ef41b7c5c5c9a7f49cffadc018d7e102e9a93663
[INFO] running `Command { std: "docker" "start" "-a" "2b2b2ce005d4d5560541a484ef41b7c5c5c9a7f49cffadc018d7e102e9a93663", kill_on_drop: false }`
[INFO] [stderr]    Compiling tower-http v0.6.8
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[INFO] [stderr]    Compiling tempfile v3.27.0
[INFO] [stderr]    Compiling reqwest v0.13.2
[INFO] [stderr]    Compiling vareffect-cli v0.1.3 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 10.12s
[INFO] running `Command { std: "docker" "inspect" "2b2b2ce005d4d5560541a484ef41b7c5c5c9a7f49cffadc018d7e102e9a93663", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "2b2b2ce005d4d5560541a484ef41b7c5c5c9a7f49cffadc018d7e102e9a93663", kill_on_drop: false }`
[INFO] [stdout] 2b2b2ce005d4d5560541a484ef41b7c5c5c9a7f49cffadc018d7e102e9a93663
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] 0ebd06ac4566c65418778d73ed240e2bdcf3683ea7c0fa5906a78f67a155b29f
[INFO] running `Command { std: "docker" "start" "-a" "0ebd06ac4566c65418778d73ed240e2bdcf3683ea7c0fa5906a78f67a155b29f", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.67s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/vareffect-540f985051bb70da)
[INFO] [stdout] 
[INFO] [stdout] running 79 tests
[INFO] [stdout] test builders::reference_genome::tests::append_extension_appends_suffix ... ok
[INFO] [stdout] test builders::transcript_models::cross_validate::tests::normalize_summary_chrom_handles_all_formats ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_attr_decodes_common_encodings ... ok
[INFO] [stdout] test builders::patch_chrom_aliases::tests::load_missing_file_hints_at_vareffect_cli_setup ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_ensembl_from_dbxref_works ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_protein_id_accepts_predicted_xp_accession ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_protein_id_falls_back_to_dbxref ... ok
[INFO] [stdout] test builders::transcript_models::cross_validate::tests::cross_validate_summary_rejects_built_primary_summary_patch ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_protein_id_from_dbxref_handles_capital_b ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_protein_id_prefers_direct_attr_over_dbxref ... ok
[INFO] [stdout] test builders::transcript_models::cross_validate::tests::cross_validate_summary_resolves_patch_alias_hit ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_refseq_acc_from_dbxref_handles_capital_b ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::percent_decode_gff3_handles_full_reserved_set ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::percent_decode_gff3_passes_through_malformed_escapes ... ok
[INFO] [stdout] test builders::transcript_models::tests::biotype_derivation_gene_biotype_overrides ... ok
[INFO] [stdout] test builders::transcript_models::tests::biotype_derivation_from_accession_prefix ... ok
[INFO] [stdout] test builders::transcript_models::tests::build_cds_segments_rejects_misaligned_cds ... ok
[INFO] [stdout] test builders::transcript_models::cross_validate::tests::cross_validate_summary_rejects_patch_alias_mismatch ... ok
[INFO] [stdout] test builders::transcript_models::tests::extract_first_parent_splits_multi_valued_parents ... ok
[INFO] [stdout] test builders::transcript_models::cross_validate::tests::cross_validate_summary_tolerates_unknown_patch_alias ... ok
[INFO] [stdout] test builders::patch_chrom_aliases::tests::load_rejects_empty_file ... ok
[INFO] [stdout] test builders::patch_chrom_aliases::tests::load_tolerates_hand_edits_and_whitespace ... ok
[INFO] [stdout] test builders::reference_genome::tests::convert_fasta_to_flat_binary_rejects_non_iupac ... ok
[INFO] [stdout] test builders::transcript_models::tests::parse_phase_accepts_valid_values ... ok
[INFO] [stdout] test builders::transcript_models::tests::parse_phase_rejects_invalid_values ... ok
[INFO] [stdout] test builders::reference_genome::tests::convert_fasta_to_flat_binary_accepts_iupac_ambiguity ... ok
[INFO] [stdout] test builders::transcript_models::tests::tier_from_attrs_detects_both_tiers ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_hgnc_from_dbxref_works ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_refseq_acc_from_dbxref_handles_legacy_lowercase_b ... ok
[INFO] [stdout] test builders::patch_chrom_aliases::tests::build_from_assembly_report_extracts_only_patch_rows_with_ucsc_names ... ok
[INFO] [stdout] test builders::reference_genome::tests::convert_fasta_to_flat_binary_round_trip ... ok
[INFO] [stdout] test builders::transcript_models::tests::parses_mane_select_with_reversed_exons_and_cds ... ok
[INFO] [stdout] test builders::transcript_models::tests::output_is_sorted_by_accession_for_determinism ... ok
[INFO] [stdout] test check::tests::check_fails_for_missing_config ... ok
[INFO] [stdout] test builders::transcript_models::tests::parses_mane_plus_clinical_plus_strand ... ok
[INFO] [stdout] test builders::reference_genome::tests::convert_fasta_to_flat_binary_uses_shared_version ... ok
[INFO] [stdout] test check::tests::check_passes_for_config_and_data_dir ... ok
[INFO] [stdout] test builders::transcript_models::tests::tier_from_attrs_accepts_comma_separated_tag_list ... ok
[INFO] [stdout] test builders::transcript_models::tests::parses_uncommon_feature_type_vault_rna ... ok
[INFO] [stdout] test builders::transcript_models::tests::tier_from_attrs_rejects_substring_false_positive ... ok
[INFO] [stdout] test builders::transcript_models::cross_validate::tests::cross_validate_summary_rejects_built_patch_summary_primary ... ok
[INFO] [stdout] test config::tests::parse_config_with_mane_section_overrides_gff_filename ... ok
[INFO] [stdout] test check::tests::manifest_record_count_missing_manifest ... ok
[INFO] [stdout] test builders::transcript_models::tests::non_mane_row_is_dropped_regardless_of_feature_type ... ok
[INFO] [stdout] test check::tests::check_passes_when_all_files_present ... ok
[INFO] [stdout] test csq::tests::format_csq_multiple_consequences ... ok
[INFO] [stdout] test csq::tests::format_csq_position_range_for_indel ... ok
[INFO] [stdout] test check::tests::manifest_record_count_read ... ok
[INFO] [stdout] test builders::transcript_models::tests::parses_patch_sequence_transcript ... ok
[INFO] [stdout] test builders::transcript_models::tests::parses_non_coding_lnc_rna_transcript ... ok
[INFO] [stdout] test config::tests::parse_ignores_unknown_sections ... ok
[INFO] [stdout] test csq::tests::format_csq_hgvsp_omitted_without_protein_accession ... ok
[INFO] [stdout] test csq::tests::format_csq_intronic_many_empty ... ok
[INFO] [stdout] test config::tests::parse_minimal_vareffect_config ... ok
[INFO] [stdout] test csq::tests::format_csq_missense_full ... ok
[INFO] [stdout] test csq::tests::format_variant_csq_all_intergenic_returns_empty ... ok
[INFO] [stdout] test csq::tests::format_variant_csq_skips_intergenic ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_complex ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_deletion ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_snv ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_shared_suffix ... ok
[INFO] [stdout] test init::tests::data_dir_override_substitutes_paths ... ok
[INFO] [stdout] test init::tests::default_template_is_identical_to_repo_file ... ok
[INFO] [stdout] test init::tests::default_template_parses_as_valid_config ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_insertion ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_multi_base_insertion ... ok
[INFO] [stdout] test init::tests::data_dir_override_produces_valid_config ... ok
[INFO] [stdout] test vcf::tests::parse_multi_allelic ... ok
[INFO] [stdout] test vcf::tests::parse_rejects_pos_zero ... ok
[INFO] [stdout] test vcf::tests::parse_simple_snv ... ok
[INFO] [stdout] test vcf::tests::parse_rejects_too_few_columns ... ok
[INFO] [stdout] test vcf::tests::write_annotated_preserves_trailing_columns ... ok
[INFO] [stdout] test vcf::tests::write_annotated_appends_to_existing_info ... ok
[INFO] [stdout] test init::tests::init_creates_parent_directories ... ok
[INFO] [stdout] test init::tests::init_creates_config_file ... ok
[INFO] [stdout] test builders::patch_chrom_aliases::tests::load_round_trips_build_output ... ok
[INFO] [stdout] test vcf::tests::write_annotated_replaces_dot_info ... ok
[INFO] [stdout] test init::tests::init_with_force_overwrites_existing ... ok
[INFO] [stdout] test csq::tests::format_variant_csq_multiple_transcripts ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 79 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.16s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "0ebd06ac4566c65418778d73ed240e2bdcf3683ea7c0fa5906a78f67a155b29f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "0ebd06ac4566c65418778d73ed240e2bdcf3683ea7c0fa5906a78f67a155b29f", kill_on_drop: false }`
[INFO] [stdout] 0ebd06ac4566c65418778d73ed240e2bdcf3683ea7c0fa5906a78f67a155b29f
