[INFO] cloning repository https://github.com/gkanogiannis/panpath-audit
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/gkanogiannis/panpath-audit" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fgkanogiannis%2Fpanpath-audit", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fgkanogiannis%2Fpanpath-audit'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 917251abd3bc5f160e9e0c5a15ef2cd6f7467e38
[INFO] testing gkanogiannis/panpath-audit against 1.99.0-beta.8+cargoflags=--release for beta-release-1.100-2
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fgkanogiannis%2Fpanpath-audit" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/gkanogiannis/panpath-audit
[INFO] finished tweaking git repo https://github.com/gkanogiannis/panpath-audit
[INFO] tweaked toml for git repo https://github.com/gkanogiannis/panpath-audit written to /workspace/builds/worker-0-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/gkanogiannis/panpath-audit 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 git repo https://github.com/gkanogiannis/panpath-audit 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] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:77db811e55d90add9212f6832c23229e3de5f1c1f9905e8cb07319ea15df73ac" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12
[INFO] running `Command { std: "docker" "start" "58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12", 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" "58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12" "/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" "58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12", 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" "58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "build" "--frozen" "--message-format=json" "--release", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.107
[INFO] [stderr]    Compiling cfg-if v1.0.4
[INFO] [stderr]    Compiling typenum v1.20.1
[INFO] [stderr]    Compiling quote v1.0.47
[INFO] [stderr]    Compiling unicode-ident v1.0.24
[INFO] [stderr]    Compiling serde_core v1.0.229
[INFO] [stderr]    Compiling libc v0.2.189
[INFO] [stderr]    Compiling shlex v2.0.1
[INFO] [stderr]    Compiling find-msvc-tools v0.1.10
[INFO] [stderr]    Compiling crc32fast v1.5.0
[INFO] [stderr]    Compiling rustix v1.1.4
[INFO] [stderr]    Compiling getrandom v0.4.3
[INFO] [stderr]    Compiling zmij v1.0.23
[INFO] [stderr]    Compiling linux-raw-sys v0.12.1
[INFO] [stderr]    Compiling bitflags v2.13.1
[INFO] [stderr]    Compiling serde_json v1.0.151
[INFO] [stderr]    Compiling adler2 v2.0.1
[INFO] [stderr]    Compiling simd-adler32 v0.3.10
[INFO] [stderr]    Compiling serde v1.0.229
[INFO] [stderr]    Compiling cpufeatures v0.2.17
[INFO] [stderr]    Compiling arrayvec v0.7.8
[INFO] [stderr]    Compiling arrayref v0.3.9
[INFO] [stderr]    Compiling once_cell v1.21.4
[INFO] [stderr]    Compiling memchr v2.8.3
[INFO] [stderr]    Compiling cc v1.4.2
[INFO] [stderr]    Compiling miniz_oxide v0.8.9
[INFO] [stderr]    Compiling fastrand v2.5.0
[INFO] [stderr]    Compiling itoa v1.0.18
[INFO] [stderr]    Compiling cpufeatures v0.3.0
[INFO] [stderr]    Compiling constant_time_eq v0.4.2
[INFO] [stderr]    Compiling flate2 v1.1.9
[INFO] [stderr]    Compiling syn v3.0.3
[INFO] [stderr]    Compiling generic-array v0.14.7
[INFO] [stderr]    Compiling blake3 v1.8.6
[INFO] [stderr]    Compiling block-buffer v0.10.4
[INFO] [stderr]    Compiling crypto-common v0.1.7
[INFO] [stderr]    Compiling digest v0.10.7
[INFO] [stderr]    Compiling sha2 v0.10.9
[INFO] [stderr]    Compiling tempfile v3.27.0
[INFO] [stderr]    Compiling serde_derive v1.0.229
[INFO] [stderr]    Compiling panpath-audit v0.1.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 28.33s
[INFO] running `Command { std: "docker" "inspect" "58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12", 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" "58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen" "--no-run" "--message-format=json" "--release", kill_on_drop: false }`
[INFO] [stderr]    Compiling panpath-audit v0.1.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 3.00s
[INFO] running `Command { std: "docker" "inspect" "58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12", 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" "58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen" "--release", kill_on_drop: false }`
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 0.08s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/release/deps/panpath_audit-1f36c7f03e240e56)
[INFO] [stdout] 
[INFO] [stdout] running 8 tests
[INFO] [stdout] test memory::tests::rejects_oversized_alignment ... ok
[INFO] [stdout] test memory::tests::tracks_peak_and_oversized_admissions ... ok
[INFO] [stdout] test statistics::tests::enforces_cell_limit ... ok
[INFO] [stdout] test statistics::tests::counts_edit_operations ... ok
[INFO] [stdout] test streaming_gfa::tests::numeric_reference_is_twelve_bytes ... ok
[INFO] [stdout] test digests::tests::normalizes_case ... ok
[INFO] [stdout] test statistics::tests::agrees_with_dynamic_programming_on_small_inputs ... ok
[INFO] [stdout] test statistics::tests::counts_literal_ambiguous_columns ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 8 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/cli.rs (/opt/rustwide/target/release/deps/cli-4da52bad05a8def0)
[INFO] [stdout] 
[INFO] [stdout] running 60 tests
[INFO] [stdout] test divergence_in_reverse_segment_reports_both_coordinates ... ok
[INFO] [stdout] test alignment_limit_uses_unavailable_buckets ... ok
[INFO] [stdout] test alignment_limit_requires_comprehensive_mode ... ok
[INFO] [stdout] test clipped_walk_reports_full_and_addressed_digests ... ok
[INFO] [stdout] test clipped_gaps_between_walk_ranges_are_ignored ... ok
[INFO] [stdout] test anonymous_scratch_files_leave_no_directory_entries ... ok
[INFO] [stdout] test comprehensive_statistics_count_indels ... ok
[INFO] [stdout] test duplicate_identifiers_across_fasta_inputs_are_rejected ... ok
[INFO] [stdout] test comprehensive_statistics_are_parallel_deterministic ... ok
[INFO] [stdout] test comprehensive_statistics_count_clipped_walk_bases ... ok
[INFO] [stdout] test duplicate_fasta_identifier_is_a_preflight_error ... ok
[INFO] [stdout] test automatic_thread_count_is_capped_at_eight ... ok
[INFO] [stdout] test comprehensive_invalid_json_has_null_statistics ... ok
[INFO] [stdout] test explicit_thread_count_is_reported ... ok
[INFO] [stdout] test gfa_preflight_reports_all_detectable_errors ... ok
[INFO] [stdout] test gfa_preflight_rejects_unreconstructable_paths ... ok
[INFO] [stdout] test invalid_tsv_uses_the_outcome_header ... ok
[INFO] [stdout] test help_exits_without_inputs ... ok
[INFO] [stdout] test double_dash_allows_paths_starting_with_hyphen ... ok
[INFO] [stdout] test full_length_walk_reconstructs_a_pansn_source ... ok
[INFO] [stdout] test audit_reports_complete_correspondence_outcomes ... ok
[INFO] [stdout] test invalid_source_symbols_are_preflight_errors ... ok
[INFO] [stdout] test gzip_fasta_is_detected_by_content ... ok
[INFO] [stdout] test comprehensive_statistics_partition_source_and_graph_bases ... ok
[INFO] [stdout] test invalid_gzip_source_symbol_is_a_source_error ... ok
[INFO] [stdout] test json_clipped_walk_reports_only_embedded_length ... ok
[INFO] [stdout] test invalid_unused_segment_blocks_the_entire_audit ... ok
[INFO] [stdout] test json_mode_emits_one_versioned_document ... ok
[INFO] [stdout] test gzip_gfa_is_streamed_and_detected_by_content ... ok
[INFO] [stdout] test json_mode_remains_valid_when_preflight_fails ... ok
[INFO] [stdout] test human_output_discloses_provenance_limits ... ok
[INFO] [stdout] test json_walk_divergence_reports_range_and_segment_coordinates ... ok
[INFO] [stdout] test identical_path_exits_zero ... ok
[INFO] [stdout] test json_identical_outcomes_report_their_record_type ... ok
[INFO] [stdout] test overlapping_walk_ranges_are_a_preflight_error ... ok
[INFO] [stdout] test json_walk_range_length_mismatch_is_structured ... ok
[INFO] [stdout] test path_and_walk_cannot_claim_the_same_identifier ... ok
[INFO] [stdout] test json_provenance_counts_path_and_walk_records ... ok
[INFO] [stdout] test pansn_and_prefix_mappings_disambiguate_reference_headers ... ok
[INFO] [stdout] test missing_source_lengths_support_forward_and_repeated_segments ... ok
[INFO] [stdout] test missing_source_walk_retains_its_record_type_in_json ... ok
[INFO] [stdout] test unspecified_walk_range_cannot_be_combined_with_another_record ... ok
[INFO] [stdout] test version_exits_without_inputs ... ok
[INFO] [stdout] test reverse_path_supports_the_complete_iupac_alphabet ... ok
[INFO] [stdout] test preflight_combines_fasta_and_gfa_errors ... ok
[INFO] [stdout] test walk_haplotype_index_must_be_numeric ... ok
[INFO] [stdout] test zero_threads_is_rejected ... ok
[INFO] [stdout] test multiple_fasta_inputs_form_one_source_set ... ok
[INFO] [stdout] test walk_range_cannot_exceed_the_source_sequence ... ok
[INFO] [stdout] test walk_ranges_are_stitched_in_coordinate_order ... ok
[INFO] [stdout] test walk_length_must_match_its_declared_range ... ok
[INFO] [stdout] test truncated_walk_record_is_a_preflight_error ... ok
[INFO] [stdout] test truncated_path_reports_exhaustion_without_segment_coordinates ... ok
[INFO] [stdout] test zero_memory_budget_is_rejected ... ok
[INFO] [stdout] test parallel_and_single_thread_outcomes_are_identical ... ok
[INFO] [stdout] test walk_is_accepted_with_legacy_gfa_1_0_header ... ok
[INFO] [stdout] test tsv_reports_outcomes_and_digests ... ok
[INFO] [stdout] test alignment_respects_memory_budget ... ok
[INFO] [stdout] test oversized_contig_runs_alone_and_is_reported ... ok
[INFO] [stdout] test memory_budget_is_reported_and_limits_concurrency ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 60 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.29s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12", kill_on_drop: false }`
[INFO] [stdout] 58c06c9e60fd10dfc5bb40c8272a7a63885801490a457082d43d7437bf46bd12