[INFO] fetching crate vareffect-cli 0.5.0...
[INFO] testing vareffect-cli-0.5.0 against 1.99.0-beta.8 for beta-1.100-2
[INFO] extracting crate vareffect-cli 0.5.0 into /workspace/builds/worker-3-tc1/source
[INFO] started tweaking crates.io crate vareffect-cli 0.5.0
[INFO] finished tweaking crates.io crate vareffect-cli 0.5.0
[INFO] tweaked toml for crates.io crate vareffect-cli 0.5.0 written to /workspace/builds/worker-3-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate vareffect-cli 0.5.0 on toolchain 1.99.0-beta.8
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.99.0-beta.8" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate vareffect-cli 0.5.0 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" "+1.99.0-beta.8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded coitrees v0.4.0
[INFO] [stderr]   Downloaded vareffect v0.5.0
[INFO] [stderr]   Downloaded noodles-bgzf v0.47.0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,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" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:3111399a4047eeb3a02b7a90e478d715f38a8c6669b5c4b49d30a17385265909" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e
[INFO] running `Command { std: "docker" "start" "08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling syn v3.0.3
[INFO] [stderr]    Compiling zeroize v1.9.0
[INFO] [stderr]    Compiling futures-sink v0.3.34
[INFO] [stderr]    Compiling futures-io v0.3.34
[INFO] [stderr]    Compiling cc v1.4.4
[INFO] [stderr]    Compiling tokio v1.53.1
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling hybrid-array v0.4.14
[INFO] [stderr]    Compiling tracing v0.1.44
[INFO] [stderr]    Compiling serde_json v1.0.151
[INFO] [stderr]    Compiling portable-atomic v1.15.0
[INFO] [stderr]    Compiling regex-automata v0.4.18
[INFO] [stderr]    Compiling zlib-rs v0.6.7
[INFO] [stderr]    Compiling clap_builder v4.6.6
[INFO] [stderr]    Compiling console v0.16.4
[INFO] [stderr]    Compiling thread_local v1.1.10
[INFO] [stderr]    Compiling futures-channel v0.3.34
[INFO] [stderr]    Compiling rustls-pki-types v1.15.1
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[INFO] [stderr]    Compiling toml_datetime v1.1.1+spec-1.1.0
[INFO] [stderr]    Compiling rustls-native-certs v0.8.4
[INFO] [stderr]    Compiling memmap2 v0.9.11
[INFO] [stderr]    Compiling serde_spanned v1.1.1
[INFO] [stderr]    Compiling coitrees v0.4.0
[INFO] [stderr]    Compiling either v1.18.0
[INFO] [stderr]    Compiling block-buffer v0.12.1
[INFO] [stderr]    Compiling crypto-common v0.2.2
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[INFO] [stderr]    Compiling rayon v1.12.0
[INFO] [stderr]    Compiling rmp v0.8.15
[INFO] [stderr]    Compiling indicatif v0.18.6
[INFO] [stderr]    Compiling cmake v0.1.58
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[INFO] [stderr]    Compiling serde_derive v1.0.229
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[INFO] [stderr]    Compiling zerovec v0.11.8
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[INFO] [stderr]    Compiling icu_locale_core v2.3.0
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[INFO] [stderr]    Compiling serde v1.0.229
[INFO] [stderr]    Compiling icu_provider v2.3.1
[INFO] [stderr]    Compiling icu_properties v2.3.0
[INFO] [stderr]    Compiling icu_normalizer v2.3.0
[INFO] [stderr]    Compiling tracing-serde v0.2.0
[INFO] [stderr]    Compiling rmp-serde v1.3.1
[INFO] [stderr]    Compiling chrono v0.4.45
[INFO] [stderr]    Compiling tracing-subscriber v0.3.23
[INFO] [stderr]    Compiling vareffect v0.5.0
[INFO] [stderr]    Compiling idna_adapter v1.2.2
[INFO] [stderr]    Compiling idna v1.1.0
[INFO] [stderr]    Compiling url v2.5.8
[INFO] [stderr]    Compiling tower-http v0.6.11
[INFO] [stderr]    Compiling aws-lc-rs v1.18.0
[INFO] [stderr]    Compiling rustls v0.23.43
[INFO] [stderr]    Compiling rustls-webpki v0.103.15
[INFO] [stderr]    Compiling tokio-rustls v0.26.4
[INFO] [stderr]    Compiling rustls-platform-verifier v0.7.0
[INFO] [stderr]    Compiling hyper-rustls v0.27.9
[INFO] [stderr]    Compiling reqwest v0.13.4
[INFO] [stderr]    Compiling vareffect-cli v0.5.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 22s
[INFO] running `Command { std: "docker" "inspect" "08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling tower-http v0.6.11
[INFO] [stderr]    Compiling reqwest v0.13.4
[INFO] [stderr]    Compiling vareffect-cli v0.5.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 9.10s
[INFO] running `Command { std: "docker" "inspect" "08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.36s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/vareffect-be85e8bf7ca14eb0)
[INFO] [stdout] 
[INFO] [stdout] running 87 tests
[INFO] [stdout] test annotate::tests::process_headers_injects_csq_immediately_before_chrom ... ok
[INFO] [stdout] test builders::patch_chrom_aliases::tests::load_rejects_empty_file ... ok
[INFO] [stdout] test annotate::tests::strip_trailing_cr_removes_one_cr ... ok
[INFO] [stdout] test builders::patch_chrom_aliases::tests::load_missing_file_hints_at_vareffect_cli_setup ... ok
[INFO] [stdout] test annotate::tests::resolve_threads_auto_is_at_least_one ... ok
[INFO] [stdout] test builders::transcript_models::cross_validate::tests::cross_validate_summary_rejects_built_primary_summary_patch ... ok
[INFO] [stdout] test builders::patch_chrom_aliases::tests::load_tolerates_hand_edits_and_whitespace ... ok
[INFO] [stdout] test builders::transcript_models::cross_validate::tests::cross_validate_summary_rejects_built_patch_summary_primary ... ok
[INFO] [stdout] test builders::reference_genome::tests::append_extension_appends_suffix ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_attr_decodes_common_encodings ... 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_ensembl_from_dbxref_works ... 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::gff3_attrs::tests::extract_refseq_acc_from_dbxref_handles_capital_b ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_hgnc_from_dbxref_works ... ok
[INFO] [stdout] test annotate::tests::process_headers_tolerates_missing_chrom ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_protein_id_accepts_predicted_xp_accession ... ok
[INFO] [stdout] test builders::reference_genome::tests::convert_fasta_to_flat_binary_rejects_non_iupac ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_refseq_acc_from_dbxref_handles_legacy_lowercase_b ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::extract_protein_id_falls_back_to_dbxref ... ok
[INFO] [stdout] test builders::transcript_models::tests::biotype_derivation_from_accession_prefix ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::percent_decode_gff3_passes_through_malformed_escapes ... ok
[INFO] [stdout] test builders::transcript_models::gff3_attrs::tests::percent_decode_gff3_handles_full_reserved_set ... ok
[INFO] [stdout] test builders::transcript_models::tests::extract_first_parent_splits_multi_valued_parents ... ok
[INFO] [stdout] test builders::transcript_models::tests::parse_phase_rejects_invalid_values ... ok
[INFO] [stdout] test builders::transcript_models::cross_validate::tests::cross_validate_summary_resolves_patch_alias_hit ... ok
[INFO] [stdout] test builders::patch_chrom_aliases::tests::load_round_trips_build_output ... ok
[INFO] [stdout] test builders::transcript_models::cross_validate::tests::cross_validate_summary_rejects_patch_alias_mismatch ... 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_uses_shared_version ... ok
[INFO] [stdout] test builders::transcript_models::tests::biotype_derivation_gene_biotype_overrides ... ok
[INFO] [stdout] test builders::reference_genome::tests::convert_fasta_to_flat_binary_round_trip ... ok
[INFO] [stdout] test builders::transcript_models::tests::parses_patch_sequence_transcript ... ok
[INFO] [stdout] test builders::transcript_models::tests::build_cds_segments_rejects_misaligned_cds ... ok
[INFO] [stdout] test builders::transcript_models::tests::parses_mane_plus_clinical_plus_strand ... 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::tests::parse_phase_accepts_valid_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::non_mane_row_is_dropped_regardless_of_feature_type ... ok
[INFO] [stdout] test builders::transcript_models::tests::parses_mane_select_with_reversed_exons_and_cds ... ok
[INFO] [stdout] test builders::transcript_models::tests::parses_non_coding_lnc_rna_transcript ... ok
[INFO] [stdout] test builders::transcript_models::tests::tier_from_attrs_accepts_comma_separated_tag_list ... 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 config::tests::parse_minimal_vareffect_config ... ok
[INFO] [stdout] test builders::transcript_models::tests::output_is_sorted_by_accession_for_determinism ... ok
[INFO] [stdout] test csq::tests::format_csq_missense_full ... ok
[INFO] [stdout] test csq::tests::format_variant_csq_multiple_transcripts ... ok
[INFO] [stdout] test check::tests::check_fails_for_missing_config ... ok
[INFO] [stdout] test csq::tests::format_csq_position_range_for_indel ... 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 check::tests::check_passes_for_config_and_data_dir ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_insertion ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_shared_suffix ... ok
[INFO] [stdout] test builders::transcript_models::tests::tier_from_attrs_detects_both_tiers ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_multi_base_insertion ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_snv ... ok
[INFO] [stdout] test csq::tests::format_csq_intronic_many_empty ... ok
[INFO] [stdout] test builders::transcript_models::tests::tier_from_attrs_rejects_substring_false_positive ... ok
[INFO] [stdout] test check::tests::manifest_record_count_missing_manifest ... ok
[INFO] [stdout] test init::tests::data_dir_override_substitutes_paths ... ok
[INFO] [stdout] test check::tests::check_passes_when_all_files_present ... ok
[INFO] [stdout] test init::tests::default_template_is_identical_to_repo_file ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_complex ... ok
[INFO] [stdout] test config::tests::parse_config_with_mane_section_overrides_gff_filename ... ok
[INFO] [stdout] test vcf::tests::parse_multi_allelic ... ok
[INFO] [stdout] test vcf::tests::parse_rejects_pos_zero ... ok
[INFO] [stdout] test init::tests::data_dir_override_produces_valid_config ... ok
[INFO] [stdout] test init::tests::default_template_parses_as_valid_config ... ok
[INFO] [stdout] test csq::tests::format_csq_multiple_consequences ... ok
[INFO] [stdout] test vcf::tests::parse_rejects_too_few_columns ... ok
[INFO] [stdout] test vcf::tests::parse_simple_snv ... ok
[INFO] [stdout] test csq::tests::trimmed_csq_allele_deletion ... ok
[INFO] [stdout] test vcf::tests::trailing_cr_corrupts_sites_only_info_if_not_stripped ... ok
[INFO] [stdout] test vcf::tests::write_annotated_appends_to_existing_info ... ok
[INFO] [stdout] test vcf::tests::write_annotated_preserves_trailing_columns ... ok
[INFO] [stdout] test vcf::tests::write_annotated_replaces_dot_info ... ok
[INFO] [stdout] test vcf::tests::write_annotated_sites_only_dot_info_replaces_cleanly ... ok
[INFO] [stdout] test init::tests::init_with_force_overwrites_existing ... ok
[INFO] [stdout] test builders::transcript_models::tests::parses_uncommon_feature_type_vault_rna ... ok
[INFO] [stdout] test init::tests::init_creates_config_file ... ok
[INFO] [stdout] test init::tests::init_creates_parent_directories ... ok
[INFO] [stdout] test vcf::tests::open_reader_reads_all_members_of_multi_member_gzip ... ok
[INFO] [stdout] test builders::transcript_models::cross_validate::tests::cross_validate_summary_tolerates_unknown_patch_alias ... ok
[INFO] [stdout] test check::tests::manifest_record_count_read ... ok
[INFO] [stdout] test vcf::tests::vcf_writer_bgzf_finish_round_trips ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 87 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.06s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e", kill_on_drop: false }`
[INFO] [stdout] 08106856e5a4f7131eedd42b334ca1b263d584e2b93c828d8bb6cad3c33fe78e
