[INFO] cloning repository https://github.com/catancs/seqfw
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/catancs/seqfw" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fcatancs%2Fseqfw", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fcatancs%2Fseqfw'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 68933f9005e15a4cf5e48c180ec94a1038bac224
[INFO] testing catancs/seqfw against 1.98.0-beta.8+cargoflags=--release for beta-release-1.99-2
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fcatancs%2Fseqfw" "/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/catancs/seqfw
[INFO] finished tweaking git repo https://github.com/catancs/seqfw
[INFO] tweaked toml for git repo https://github.com/catancs/seqfw written to /workspace/builds/worker-0-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/catancs/seqfw on toolchain 1.98.0-beta.8
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.98.0-beta.8" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/catancs/seqfw 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" "+1.98.0-beta.8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded pyo3-build-config v0.23.5
[INFO] [stderr]   Downloaded pyo3-ffi v0.23.5
[INFO] [stderr]   Downloaded pyo3-macros v0.23.5
[INFO] [stderr]   Downloaded assert_cmd v2.2.2
[INFO] [stderr]   Downloaded pyo3-macros-backend v0.23.5
[INFO] [stderr]   Downloaded pyo3 v0.23.5
[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@sha256:8683fc1fc2eb5c9ac98e0d076ab094b2ffac7f99da555d2b6a2e27f346de2ec7" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80
[INFO] running `Command { std: "docker" "start" "01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80", 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" "01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80" "/opt/rustwide/cargo-home/bin/cargo" "+1.98.0-beta.8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80", 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" "01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80" "/opt/rustwide/cargo-home/bin/cargo" "+1.98.0-beta.8" "build" "--frozen" "--message-format=json" "--release", kill_on_drop: false }`
[INFO] [stderr]    Compiling syn v2.0.117
[INFO] [stderr]    Compiling serde_core v1.0.228
[INFO] [stderr]    Compiling simd-adler32 v0.3.9
[INFO] [stderr]    Compiling serde_json v1.0.150
[INFO] [stderr]    Compiling memchr v2.8.1
[INFO] [stderr]    Compiling clap_builder v4.6.0
[INFO] [stderr]    Compiling miniz_oxide v0.8.9
[INFO] [stderr]    Compiling flate2 v1.1.9
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling clap_derive v4.6.1
[INFO] [stderr]    Compiling clap v4.6.1
[INFO] [stderr]    Compiling serde v1.0.228
[INFO] [stderr]    Compiling seqfw-core v0.1.0 (/opt/rustwide/workdir/crates/seqfw-core)
[INFO] [stderr]    Compiling seqfw-cli v0.1.0 (/opt/rustwide/workdir/crates/seqfw-cli)
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 18.60s
[INFO] running `Command { std: "docker" "inspect" "01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80", 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" "01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80" "/opt/rustwide/cargo-home/bin/cargo" "+1.98.0-beta.8" "test" "--frozen" "--no-run" "--message-format=json" "--release", kill_on_drop: false }`
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling aho-corasick v1.1.4
[INFO] [stderr]    Compiling predicates-core v1.0.10
[INFO] [stderr]    Compiling normalize-line-endings v0.3.0
[INFO] [stderr]    Compiling assert_cmd v2.2.2
[INFO] [stderr]    Compiling difflib v0.4.0
[INFO] [stderr]    Compiling wait-timeout v0.2.1
[INFO] [stderr]    Compiling seqfw-core v0.1.0 (/opt/rustwide/workdir/crates/seqfw-core)
[INFO] [stderr]    Compiling predicates-tree v1.0.13
[INFO] [stderr]    Compiling float-cmp v0.10.0
[INFO] [stderr]    Compiling regex-automata v0.4.14
[INFO] [stderr]    Compiling regex v1.12.4
[INFO] [stderr]    Compiling bstr v1.12.1
[INFO] [stderr]    Compiling predicates v3.1.4
[INFO] [stderr]    Compiling seqfw-cli v0.1.0 (/opt/rustwide/workdir/crates/seqfw-cli)
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 18.13s
[INFO] running `Command { std: "docker" "inspect" "01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80", 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" "01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80" "/opt/rustwide/cargo-home/bin/cargo" "+1.98.0-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/seqfw-d2b01acd7dcb09d3)
[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]      Running tests/cli.rs (/opt/rustwide/target/release/deps/cli-6d5ceb05dd020fb1)
[INFO] [stdout] 
[INFO] [stdout] running 18 tests
[INFO] [stdout] test check_clean_file_exits_zero ... ok
[INFO] [stdout] test check_good_fasta_exits_zero ... ok
[INFO] [stdout] test check_good_vcf_exits_zero ... ok
[INFO] [stdout] test check_json_reports_findings ... ok
[INFO] [stdout] test check_bad_pos_vcf_exits_one ... ok
[INFO] [stdout] test header_shell_metachar_warns_but_passes ... ok
[INFO] [stdout] test check_duplicate_fasta_name_exits_one ... ok
[INFO] [stdout] test check_matched_pair_exits_zero ... ok
[INFO] [stdout] test check_mismatched_pair_exits_one ... ok
[INFO] [stdout] test check_unrecognized_format_exits_one ... ok
[INFO] [stdout] test check_strict_dna_rejects_iupac ... ok
[INFO] [stdout] test forcing_fastq_on_a_fasta_file_rejects ... ok
[INFO] [stdout] test check_length_mismatch_exits_one ... ok
[INFO] [stdout] test check_format_mismatch_vcf_exits_one ... ok
[INFO] [stdout] test check_valid_fai_with_data_exits_zero ... ok
[INFO] [stdout] test check_bad_file_exits_one ... ok
[INFO] [stdout] test check_missing_file_exits_two ... ok
[INFO] [stdout] test check_out_of_bounds_fai_exits_one ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 18 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.06s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/release/deps/seqfw_core-5e57d6f65b628e1b)
[INFO] [stdout] 
[INFO] [stdout] running 68 tests
[INFO] [stdout] test bomb::tests::bomb_guard_trips_on_absolute_cap ... ok
[INFO] [stdout] test bomb::tests::bomb_guard_trips_on_ratio_cap ... ok
[INFO] [stdout] test checks::fasta::tests::empty_name_is_rejected ... ok
[INFO] [stdout] test checks::fasta::tests::empty_sequence_is_rejected ... ok
[INFO] [stdout] test checks::fasta::tests::fasta_header_shell_metachar_warns ... ok
[INFO] [stdout] test checks::fasta::tests::duplicate_name_is_rejected ... ok
[INFO] [stdout] test checks::fasta::tests::fasta_is_routed_via_sniffer ... ok
[INFO] [stdout] test checks::fasta::tests::valid_fasta_passes ... ok
[INFO] [stdout] test checks::fasta::tests::sequence_before_header_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::all_high_quality_flags_ambiguous_encoding ... ok
[INFO] [stdout] test checks::fastq::tests::bad_header_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::bad_separator_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::embedded_nul_in_sequence_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::header_shell_metachar_warns_but_passes ... ok
[INFO] [stdout] test checks::fastq::tests::invalid_base_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::iupac_ambiguity_code_passes_by_default ... ok
[INFO] [stdout] test checks::fastq::tests::low_quality_byte_suppresses_ambiguous_flag ... ok
[INFO] [stdout] test checks::fastq::tests::length_mismatch_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::pair_id_mismatch_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::matched_pair_passes ... ok
[INFO] [stdout] test checks::fastq::tests::phred_out_of_range_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::header_control_byte_is_rejected ... ok
[INFO] [stdout] test checks::index::tests::bad_magic_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::strict_dna_rejects_iupac_code ... ok
[INFO] [stdout] test checks::index::tests::gzi_offset_past_data_end_is_rejected ... ok
[INFO] [stdout] test checks::index::tests::impossible_csi_n_ref_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::truncated_record_is_rejected ... ok
[INFO] [stdout] test checks::index::tests::impossible_n_ref_is_rejected ... ok
[INFO] [stdout] test checks::index::tests::impossible_gzi_count_is_rejected ... ok
[INFO] [stdout] test checks::index::tests::non_monotonic_gzi_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::valid_fastq_passes ... ok
[INFO] [stdout] test checks::index::tests::non_numeric_field_is_rejected ... ok
[INFO] [stdout] test checks::index::tests::offset_past_end_is_rejected ... ok
[INFO] [stdout] test checks::fastq::tests::pair_count_mismatch_is_rejected ... ok
[INFO] [stdout] test checks::index::tests::impossible_name_block_is_rejected ... ok
[INFO] [stdout] test checks::index::tests::valid_csi_header_passes ... ok
[INFO] [stdout] test checks::index::tests::valid_fai_passes ... ok
[INFO] [stdout] test checks::index::tests::valid_gzi_passes ... ok
[INFO] [stdout] test checks::index::tests::valid_tbi_header_passes ... ok
[INFO] [stdout] test checks::index::tests::wrong_column_count_is_rejected ... ok
[INFO] [stdout] test checks::safety::tests::clean_identifier_has_no_findings ... ok
[INFO] [stdout] test checks::index::tests::oversized_gzi_is_rejected ... ok
[INFO] [stdout] test checks::safety::tests::path_traversal_is_flagged ... ok
[INFO] [stdout] test checks::safety::tests::shell_metachar_is_a_warning ... ok
[INFO] [stdout] test checks::safety::tests::control_byte_is_an_error ... ok
[INFO] [stdout] test checks::vcf::tests::declared_info_and_format_pass ... ok
[INFO] [stdout] test checks::vcf::tests::extra_sample_subfields_is_rejected ... ok
[INFO] [stdout] test checks::safety::tests::url_scheme_is_flagged ... ok
[INFO] [stdout] test checks::vcf::tests::fewer_sample_subfields_is_allowed ... ok
[INFO] [stdout] test checks::vcf::tests::minimal_valid_vcf_passes ... ok
[INFO] [stdout] test checks::vcf::tests::missing_fileformat_is_rejected ... ok
[INFO] [stdout] test checks::vcf::tests::column_count_mismatch_is_rejected ... ok
[INFO] [stdout] test checks::vcf::tests::non_numeric_pos_is_rejected ... ok
[INFO] [stdout] test checks::vcf::tests::undeclared_format_warns ... ok
[INFO] [stdout] test checks::vcf::tests::data_before_header_is_rejected ... ok
[INFO] [stdout] test checks::vcf::tests::vcf_is_routed_via_sniffer ... ok
[INFO] [stdout] test checks::vcf::tests::well_formed_record_passes ... ok
[INFO] [stdout] test dispatch::empty_input_is_clean ... ok
[INFO] [stdout] test dispatch::fastq_is_routed_and_passes ... ok
[INFO] [stdout] test dispatch::leading_blank_lines_are_skipped ... ok
[INFO] [stdout] test checks::vcf::tests::too_few_columns_is_rejected ... ok
[INFO] [stdout] test dispatch::unrecognized_input_is_rejected ... ok
[INFO] [stdout] test source::tests::gzipped_valid_fastq_passes ... ok
[INFO] [stdout] test checks::vcf::tests::undeclared_info_warns ... ok
[INFO] [stdout] test checks::vcf::tests::unsafe_sample_name_is_flagged ... ok
[INFO] [stdout] test smoke::version_is_set ... ok
[INFO] [stdout] test finding::tests::report_ok_only_when_no_errors ... ok
[INFO] [stdout] test source::tests::gzip_bomb_is_rejected ... ok
[INFO] [stderr]    Doc-tests seqfw_core
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 68 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.04s
[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] running `Command { std: "docker" "inspect" "01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80", kill_on_drop: false }`
[INFO] [stdout] 01476590b000119370a3fa76d40e1c731addaa5b2550bd148ac980db0b093a80