[INFO] fetching crate rsomics-annotation 0.1.0...
[INFO] testing rsomics-annotation-0.1.0 against 1.99.0-beta.8 for beta-1.100-2
[INFO] extracting crate rsomics-annotation 0.1.0 into /workspace/builds/worker-5-tc1/source
[INFO] started tweaking crates.io crate rsomics-annotation 0.1.0
[INFO] removed 0 missing tests
[INFO] finished tweaking crates.io crate rsomics-annotation 0.1.0
[INFO] tweaked toml for crates.io crate rsomics-annotation 0.1.0 written to /workspace/builds/worker-5-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate rsomics-annotation 0.1.0 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 rsomics-annotation 0.1.0 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]  Downloading crates ...
[INFO] [stderr]   Downloaded rsomics-help v0.4.0
[INFO] [stderr]   Downloaded noodles-gtf v0.50.0
[INFO] [stderr]   Downloaded rsomics-intervals v0.3.0
[INFO] [stderr]   Downloaded rsomics-common v0.11.0
[INFO] [stderr]   Downloaded noodles-gff v0.55.0
[INFO] [stderr]   Downloaded noodles-core v0.19.0
[INFO] [stderr]   Downloaded lexical-parse-integer v1.0.6
[INFO] [stderr]   Downloaded lexical-core v1.0.6
[INFO] [stderr]   Downloaded noodles-fasta v0.59.0
[INFO] [stderr]   Downloaded noodles-bgzf v0.46.0
[INFO] [stderr]   Downloaded noodles-csi v0.54.0
[INFO] [stderr]   Downloaded lexical-write-integer v1.0.6
[INFO] [stderr]   Downloaded crossbeam-channel v0.5.16
[INFO] [stderr]   Downloaded lexical-write-float v1.0.6
[INFO] [stderr]   Downloaded lexical-util v1.0.7
[INFO] [stderr]   Downloaded lexical-parse-float v1.0.6
[INFO] [stderr]   Downloaded bstr v1.13.0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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] 53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9
[INFO] running `Command { std: "docker" "start" "53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9", 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" "53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9" "/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" "53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9", 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" "53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling crossbeam-utils v0.8.22
[INFO] [stderr]    Compiling rustix v1.1.4
[INFO] [stderr]    Compiling proc-macro2 v1.0.107
[INFO] [stderr]    Compiling linux-raw-sys v0.12.1
[INFO] [stderr]    Compiling bitflags v2.13.1
[INFO] [stderr]    Compiling lexical-util v1.0.7
[INFO] [stderr]    Compiling zlib-rs v0.6.6
[INFO] [stderr]    Compiling colorchoice v1.0.5
[INFO] [stderr]    Compiling anstyle v1.0.14
[INFO] [stderr]    Compiling bstr v1.13.0
[INFO] [stderr]    Compiling anstyle-parse v1.0.0
[INFO] [stderr]    Compiling thiserror v2.0.19
[INFO] [stderr]    Compiling clap_lex v1.1.0
[INFO] [stderr]    Compiling indexmap v2.14.0
[INFO] [stderr]    Compiling bit-vec v0.8.0
[INFO] [stderr]    Compiling once_cell v1.21.4
[INFO] [stderr]    Compiling fastrand v2.5.0
[INFO] [stderr]    Compiling anstream v1.0.0
[INFO] [stderr]    Compiling lexical-write-integer v1.0.6
[INFO] [stderr]    Compiling lexical-parse-integer v1.0.6
[INFO] [stderr]    Compiling quote v1.0.47
[INFO] [stderr]    Compiling noodles-core v0.19.0
[INFO] [stderr]    Compiling crossbeam-channel v0.5.16
[INFO] [stderr]    Compiling lexical-parse-float v1.0.6
[INFO] [stderr]    Compiling syn v3.0.3
[INFO] [stderr]    Compiling lexical-write-float v1.0.6
[INFO] [stderr]    Compiling lexical-core v1.0.6
[INFO] [stderr]    Compiling terminal_size v0.4.4
[INFO] [stderr]    Compiling tempfile v3.27.0
[INFO] [stderr]    Compiling clap_builder v4.6.2
[INFO] [stderr]    Compiling thiserror-impl v2.0.19
[INFO] [stderr]    Compiling clap_derive v4.6.4
[INFO] [stderr]    Compiling serde_derive v1.0.229
[INFO] [stderr]    Compiling flate2 v1.1.9
[INFO] [stderr]    Compiling noodles-bgzf v0.46.0
[INFO] [stderr]    Compiling rsomics-intervals v0.3.0
[INFO] [stderr]    Compiling noodles-csi v0.54.0
[INFO] [stderr]    Compiling noodles-fasta v0.59.0
[INFO] [stderr]    Compiling clap v4.6.4
[INFO] [stderr]    Compiling rsomics-help v0.4.0
[INFO] [stderr]    Compiling noodles-gff v0.55.0
[INFO] [stderr]    Compiling noodles-gtf v0.50.0
[INFO] [stderr]    Compiling serde v1.0.229
[INFO] [stderr]    Compiling rsomics-common v0.11.0
[INFO] [stderr]    Compiling rsomics-annotation v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 19.55s
[INFO] running `Command { std: "docker" "inspect" "53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9", 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" "53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9" "/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 rsomics-annotation v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 1.52s
[INFO] running `Command { std: "docker" "inspect" "53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9", 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" "53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9" "/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 0.05s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/rsomics_annotation-4a689da81166b8fd)
[INFO] [stdout] 
[INFO] [stdout] running 26 tests
[INFO] [stdout] test annotation::tests::blank_lines_are_ignored ... ok
[INFO] [stdout] test annotation::tests::inverted_coordinates_fail_with_line_number ... ok
[INFO] [stdout] test annotation::tests::one_base_feature_converts_to_half_open_interval ... ok
[INFO] [stdout] test fasta::tests::empty_sequences_are_not_written ... ok
[INFO] [stdout] test splice::tests::reverse_strand_reorders_exons_and_complements_bases ... ok
[INFO] [stdout] test translation::tests::retains_nonterminal_stops_and_drops_partial_codons ... ok
[INFO] [stdout] test genome::tests::builds_an_in_memory_index_when_fai_is_absent ... ok
[INFO] [stdout] test transcript::tests::derives_exons_from_coding_segments ... ok
[INFO] [stdout] test fasta::tests::wraps_at_seventy_columns ... ok
[INFO] [stdout] test cli::tests::command_tree_is_valid ... ok
[INFO] [stdout] test transcript::tests::rejects_conflicting_transcript_sequences ... ok
[INFO] [stdout] test translation::tests::translates_standard_and_degenerate_codons ... ok
[INFO] [stdout] test cli::tests::contained_requires_region ... ok
[INFO] [stdout] test validate::tests::discontinuous_id_with_consistent_identity_is_valid ... ok
[INFO] [stdout] test validate::tests::gff_version_must_precede_comments_and_records ... ok
[INFO] [stdout] test validate::tests::gtf_stop_codon_frame_is_valid ... ok
[INFO] [stdout] test validate::tests::non_cds_phase_fails ... ok
[INFO] [stdout] test validate::tests::multiple_parents_resolve ... ok
[INFO] [stdout] test validate::tests::phased_cds_is_valid ... ok
[INFO] [stdout] test validate::tests::unresolved_parent_fails ... ok
[INFO] [stdout] test view::tests::inclusive_range_touches_both_edges ... ok
[INFO] [stdout] test validate::tests::gtf_requires_transcript_id_for_exons ... ok
[INFO] [stdout] test view::tests::zero_coordinate_is_rejected ... ok
[INFO] [stdout] test validate::tests::incompatible_duplicate_id_fails ... ok
[INFO] [stdout] test view::tests::percent_encoded_attribute_matches_decoded_value ... ok
[INFO] [stdout] test cli::tests::global_options_are_limited_to_shared_output ... ok
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/rsomics_annotation-a7bf1a64e5590e60)
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 26 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[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] [stderr]      Running tests/cli.rs (/opt/rustwide/target/debug/deps/cli-4b6071b4c286148f)
[INFO] [stdout] 
[INFO] [stdout] running 8 tests
[INFO] [stdout] test validation_failure_is_loud_and_plain ... ok
[INFO] [stdout] test invalid_cli_exits_with_status_two ... ok
[INFO] [stdout] test json_requires_a_named_data_output ... ok
[INFO] [stdout] test failed_named_output_is_transactional ... ok
[INFO] [stdout] test validates_gff3_and_gtf ... ok
[INFO] [stdout] test to_bed_uses_checked_half_open_boundary ... ok
[INFO] [stdout] test view_combines_type_attribute_and_region ... ok
[INFO] [stdout] test output_aliases_never_modify_input ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 8 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/extract.rs (/opt/rustwide/target/debug/deps/extract-d0731f8e28670381)
[INFO] [stdout] 
[INFO] [stdout] running 4 tests
[INFO] [stdout] test malformed_input_rolls_back_every_extract_output ... ok
[INFO] [stdout] test extract_paths_must_be_distinct_named_files ... ok
[INFO] [stdout] test split_gtf_stop_codon_extends_the_coding_sequence ... ok
[INFO] [stdout] test gff3_and_gtf_match_extraction_goldens ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 4 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.02s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/oracle.rs (/opt/rustwide/target/debug/deps/oracle-0630ec031758a25c)
[INFO] [stdout] 
[INFO] [stdout] running 3 tests
[INFO] [stdout] test region_overlap_matches_gffread_0_12_9 ... ok
[INFO] [stdout] test sequence_extraction_matches_gffread_0_12_9 ... ok
[INFO] [stdout] test transcript_bed_coordinates_match_gffread_0_12_9 ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 3 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9", kill_on_drop: false }`
[INFO] [stdout] 53c1dfcab35e8d310937b95f53aa7e0055a42f6763096cfa9fcf63864d50bab9
