[INFO] fetching crate sigalign 0.3.2...
[INFO] testing sigalign-0.3.2 against 1.76.0 for beta-1.77-1
[INFO] extracting crate sigalign 0.3.2 into /workspace/builds/worker-4-tc1/source
[INFO] validating manifest of crates.io crate sigalign 0.3.2 on toolchain 1.76.0
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.76.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking crates.io crate sigalign 0.3.2
[INFO] finished tweaking crates.io crate sigalign 0.3.2
[INFO] tweaked toml for crates.io crate sigalign 0.3.2 written to /workspace/builds/worker-4-tc1/source/Cargo.toml
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.76.0" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.76.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded bio-types v1.0.1
[INFO] [stderr]   Downloaded seq_io v0.3.2
[INFO] [stderr]   Downloaded enum-map v1.1.1
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[INFO] [stderr]   Downloaded capwriter v0.2.0
[INFO] [stderr]   Downloaded lt-fm-index v0.7.0-alpha.2
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[INFO] [stderr]    Compiling sigalign v0.3.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 19.97s
[INFO] running `Command { std: "docker" "inspect" "25ebe123ee7d83e5509c3b74f31f81038709f51ec231949c8f6552bd457b4def", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "25ebe123ee7d83e5509c3b74f31f81038709f51ec231949c8f6552bd457b4def", kill_on_drop: false }`
[INFO] [stdout] 25ebe123ee7d83e5509c3b74f31f81038709f51ec231949c8f6552bd457b4def
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+1.76.0" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] e250a3171938a85f06a3a1a55d93670442667ac6a521c738d291149826689588
[INFO] running `Command { std: "docker" "start" "-a" "e250a3171938a85f06a3a1a55d93670442667ac6a521c738d291149826689588", kill_on_drop: false }`
[INFO] [stderr]    Compiling sigalign v0.3.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 1.20s
[INFO] running `Command { std: "docker" "inspect" "e250a3171938a85f06a3a1a55d93670442667ac6a521c738d291149826689588", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e250a3171938a85f06a3a1a55d93670442667ac6a521c738d291149826689588", kill_on_drop: false }`
[INFO] [stdout] e250a3171938a85f06a3a1a55d93670442667ac6a521c738d291149826689588
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+1.76.0" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] 00a946da62ac8a36ef7eb90e6eb8e1dba2351f7d82e5c715baeebdf1c39e7d25
[INFO] running `Command { std: "docker" "start" "-a" "00a946da62ac8a36ef7eb90e6eb8e1dba2351f7d82e5c715baeebdf1c39e7d25", kill_on_drop: false }`
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 0.05s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/sigalign-c4ae4b53a94dc715)
[INFO] [stdout] 
[INFO] [stdout] running 3 tests
[INFO] [stdout] test aligner::regulator::tests::test_gcd_calculation_for_penalties ... ok
[INFO] [stdout] test algorithm::wave_front::fill::tests::test_if_the_default_value_of_component_is_filled_with_zero ... ok
[INFO] [stdout] test utils::file_reader::tests::test_reading_fasta_from_bytes ... 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] [stderr]    Doc-tests sigalign
[INFO] [stdout] 
[INFO] [stdout] running 9 tests
[INFO] [stdout] test src/reference/mod.rs - reference (line 75) ... FAILED
[INFO] [stdout] test src/reference/mod.rs - reference (line 61) ... FAILED
[INFO] [stdout] test src/aligner/mod.rs - aligner (line 78) ... FAILED
[INFO] [stdout] test src/reference/mod.rs - reference (line 90) ... FAILED
[INFO] [stdout] test src/aligner/mod.rs - aligner (line 89) ... FAILED
[INFO] [stdout] test src/aligner/mod.rs - aligner (line 66) ... FAILED
[INFO] [stdout] test src/lib.rs - (line 7) ... FAILED
[INFO] [stdout] test src/reference/mod.rs - reference (line 98) ... FAILED
[INFO] [stdout] test src/reference/mod.rs - reference (line 29) ... ok
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout] 
[INFO] [stdout] ---- src/reference/mod.rs - reference (line 75) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:76:27
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut sequence_buffer = reference.get_sequence_buffer();
[INFO] [stdout]   |                           ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:78:5
[INFO] [stdout]   |
[INFO] [stdout] 5 |     aligner.alignment(
[INFO] [stdout]   |     ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:79:10
[INFO] [stdout]   |
[INFO] [stdout] 6 |         &reference,
[INFO] [stdout]   |          ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/reference/mod.rs - reference (line 61) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:62:14
[INFO] [stdout]   |
[INFO] [stdout] 3 | let result = aligner.align_query(
[INFO] [stdout]   |              ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:63:6
[INFO] [stdout]   |
[INFO] [stdout] 4 |     &reference,
[INFO] [stdout]   |      ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:67:14
[INFO] [stdout]   |
[INFO] [stdout] 8 | let result = aligner.align_fasta_file(
[INFO] [stdout]   |              ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:68:6
[INFO] [stdout]   |
[INFO] [stdout] 9 |     &reference,
[INFO] [stdout]   |      ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 4 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/aligner/mod.rs - aligner (line 78) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:79:27
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut sequence_buffer = reference.get_sequence_buffer();
[INFO] [stdout]   |                           ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:81:5
[INFO] [stdout]   |
[INFO] [stdout] 5 |     aligner.alignment(
[INFO] [stdout]   |     ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:82:10
[INFO] [stdout]   |
[INFO] [stdout] 6 |         &reference,
[INFO] [stdout]   |          ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/reference/mod.rs - reference (line 90) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:91:21
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut reference = reference;
[INFO] [stdout]   |                     ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/aligner/mod.rs - aligner (line 89) stdout ----
[INFO] [stdout] error[E0412]: cannot find type `AlignmentResult` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:90:13
[INFO] [stdout]   |
[INFO] [stdout] 3 | let result: AlignmentResult = aligner.align_query(
[INFO] [stdout]   |             ^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::results::AlignmentResult;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:90:31
[INFO] [stdout]   |
[INFO] [stdout] 3 | let result: AlignmentResult = aligner.align_query(
[INFO] [stdout]   |                               ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:91:6
[INFO] [stdout]   |
[INFO] [stdout] 4 |     &reference,
[INFO] [stdout]   |      ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `FastaAlignmentResult` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:94:13
[INFO] [stdout]   |
[INFO] [stdout] 7 | let result: FastaAlignmentResult = aligner.align_fasta_file(
[INFO] [stdout]   |             ^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::results::fasta::FastaAlignmentResult;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:94:36
[INFO] [stdout]   |
[INFO] [stdout] 7 | let result: FastaAlignmentResult = aligner.align_fasta_file(
[INFO] [stdout]   |                                    ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:95:6
[INFO] [stdout]   |
[INFO] [stdout] 8 |     &reference,
[INFO] [stdout]   |      ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 6 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0412, E0425.
[INFO] [stdout] For more information about an error, try `rustc --explain E0412`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/aligner/mod.rs - aligner (line 66) stdout ----
[INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Aligner`
[INFO] [stdout]  --> src/aligner/mod.rs:67:19
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut aligner = Aligner::<LocalMode, LinearStrategy>::new(
[INFO] [stdout]   |                   ^^^^^^^ use of undeclared type `Aligner`
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::aligner::Aligner;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `LocalMode` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:67:29
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut aligner = Aligner::<LocalMode, LinearStrategy>::new(
[INFO] [stdout]   |                             ^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::aligner::mode::LocalMode;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `LinearStrategy` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:67:40
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut aligner = Aligner::<LocalMode, LinearStrategy>::new(
[INFO] [stdout]   |                                        ^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::aligner::allocation_strategy::LinearStrategy;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0412, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0412`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/lib.rs - (line 7) stdout ----
[INFO] [stdout] error[E0599]: no method named `unwrap` found for struct `AlignmentResult` in the current scope
[INFO] [stdout]   --> src/lib.rs:33:53
[INFO] [stdout]    |
[INFO] [stdout] 29 | let result = aligner.align_query(&reference, query).unwrap();
[INFO] [stdout]    |                                                     ^^^^^^ method not found in `AlignmentResult`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0599`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/reference/mod.rs - reference (line 98) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:102:1
[INFO] [stdout]   |
[INFO] [stdout] 7 | reference.save_to(&mut buffer).unwrap();
[INFO] [stdout]   | ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `buffer` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:102:24
[INFO] [stdout]   |
[INFO] [stdout] 7 | reference.save_to(&mut buffer).unwrap();
[INFO] [stdout]   |                        ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Reference`
[INFO] [stdout]  --> src/reference/mod.rs:104:17
[INFO] [stdout]   |
[INFO] [stdout] 9 | let reference = Reference::<Lfi32B2V64, InMemoryStorage>::load_from(&buffer[..]).unwrap();
[INFO] [stdout]   |                 ^^^^^^^^^ use of undeclared type `Reference`
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::reference::Reference;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `Lfi32B2V64` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:104:29
[INFO] [stdout]   |
[INFO] [stdout] 9 | let reference = Reference::<Lfi32B2V64, InMemoryStorage>::load_from(&buffer[..]).unwrap();
[INFO] [stdout]   |                             ^^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this type alias
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::reference::pattern_index::lfi::Lfi32B2V64;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `InMemoryStorage` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:104:41
[INFO] [stdout]   |
[INFO] [stdout] 9 | let reference = Reference::<Lfi32B2V64, InMemoryStorage>::load_from(&buffer[..]).unwrap();
[INFO] [stdout]   |                                         ^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::reference::sequence_storage::in_memory::InMemoryStorage;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `buffer` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:104:70
[INFO] [stdout]   |
[INFO] [stdout] 9 | let reference = Reference::<Lfi32B2V64, InMemoryStorage>::load_from(&buffer[..]).unwrap();
[INFO] [stdout]   |                                                                      ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 6 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0412, E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0412`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout]     src/aligner/mod.rs - aligner (line 66)
[INFO] [stdout]     src/aligner/mod.rs - aligner (line 78)
[INFO] [stdout]     src/aligner/mod.rs - aligner (line 89)
[INFO] [stdout]     src/lib.rs - (line 7)
[INFO] [stdout]     src/reference/mod.rs - reference (line 61)
[INFO] [stdout]     src/reference/mod.rs - reference (line 75)
[INFO] [stdout]     src/reference/mod.rs - reference (line 90)
[INFO] [stdout]     src/reference/mod.rs - reference (line 98)
[INFO] [stdout] 
[INFO] [stdout] test result: FAILED. 1 passed; 8 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.77s
[INFO] [stdout] 
[INFO] [stderr] error: doctest failed, to rerun pass `--doc`
[INFO] running `Command { std: "docker" "inspect" "00a946da62ac8a36ef7eb90e6eb8e1dba2351f7d82e5c715baeebdf1c39e7d25", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "00a946da62ac8a36ef7eb90e6eb8e1dba2351f7d82e5c715baeebdf1c39e7d25", kill_on_drop: false }`
[INFO] [stdout] 00a946da62ac8a36ef7eb90e6eb8e1dba2351f7d82e5c715baeebdf1c39e7d25
[INFO] testing sigalign-0.3.2 against beta-2024-02-10 for beta-1.77-1
[INFO] extracting crate sigalign 0.3.2 into /workspace/builds/worker-4-tc2/source
[INFO] validating manifest of crates.io crate sigalign 0.3.2 on toolchain beta-2024-02-10
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2024-02-10" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking crates.io crate sigalign 0.3.2
[INFO] finished tweaking crates.io crate sigalign 0.3.2
[INFO] tweaked toml for crates.io crate sigalign 0.3.2 written to /workspace/builds/worker-4-tc2/source/Cargo.toml
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2024-02-10" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2024-02-10" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-02-10" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] e44d06043980bf077e7d8b148f99ff5f2e9ac15fe84322412689f33b22453218
[INFO] running `Command { std: "docker" "start" "-a" "e44d06043980bf077e7d8b148f99ff5f2e9ac15fe84322412689f33b22453218", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "e44d06043980bf077e7d8b148f99ff5f2e9ac15fe84322412689f33b22453218", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e44d06043980bf077e7d8b148f99ff5f2e9ac15fe84322412689f33b22453218", kill_on_drop: false }`
[INFO] [stdout] e44d06043980bf077e7d8b148f99ff5f2e9ac15fe84322412689f33b22453218
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-02-10" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 2ca5d863e22878d0febd2830cc88fe78a6a7415dbf526eb06653665964bc6e67
[INFO] running `Command { std: "docker" "start" "-a" "2ca5d863e22878d0febd2830cc88fe78a6a7415dbf526eb06653665964bc6e67", kill_on_drop: false }`
[INFO] [stderr]    Compiling libm v0.2.8
[INFO] [stderr]    Compiling version_check v0.9.4
[INFO] [stderr]    Compiling libc v0.2.153
[INFO] [stderr]    Compiling num-traits v0.2.18
[INFO] [stderr]    Compiling num-bigint v0.4.4
[INFO] [stderr]    Compiling num-rational v0.4.1
[INFO] [stderr]    Compiling syn v2.0.48
[INFO] [stderr]    Compiling matrixmultiply v0.3.8
[INFO] [stderr]    Compiling rustversion v1.0.14
[INFO] [stderr]    Compiling paste v1.0.14
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling rawpointer v0.2.1
[INFO] [stderr]    Compiling typenum v1.17.0
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling getrandom v0.2.12
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling rand_core v0.6.4
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling aho-corasick v1.1.2
[INFO] [stderr]    Compiling cc v1.0.85
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling heck v0.4.1
[INFO] [stderr]    Compiling regex-syntax v0.8.2
[INFO] [stderr]    Compiling rand v0.8.5
[INFO] [stderr]    Compiling num-integer v0.1.46
[INFO] [stderr]    Compiling num-complex v0.4.5
[INFO] [stderr]    Compiling approx v0.5.1
[INFO] [stderr]    Compiling thiserror v1.0.57
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]    Compiling rand_distr v0.4.3
[INFO] [stderr]    Compiling cmake v0.1.50
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling byteorder v1.5.0
[INFO] [stderr]    Compiling hashbrown v0.14.3
[INFO] [stderr]    Compiling anyhow v1.0.79
[INFO] [stderr]    Compiling regex-automata v0.4.5
[INFO] [stderr]    Compiling bytemuck_derive v1.5.0
[INFO] [stderr]    Compiling serde_derive v1.0.196
[INFO] [stderr]    Compiling thiserror-impl v1.0.57
[INFO] [stderr]    Compiling equivalent v1.0.1
[INFO] [stderr]    Compiling indexmap v2.2.3
[INFO] [stderr]    Compiling strum_macros v0.25.3
[INFO] [stderr]    Compiling libdivsufsort-rs v0.1.2
[INFO] [stderr]    Compiling bytemuck v1.14.3
[INFO] [stderr]    Compiling safe_arch v0.7.1
[INFO] [stderr]    Compiling enum-map-derive v0.6.0
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling wide v0.7.15
[INFO] [stderr]    Compiling csv-core v0.1.11
[INFO] [stderr]    Compiling bit-vec v0.6.3
[INFO] [stderr]    Compiling regex v1.10.3
[INFO] [stderr]    Compiling fixedbitset v0.4.2
[INFO] [stderr]    Compiling either v1.10.0
[INFO] [stderr]    Compiling crossbeam-utils v0.8.19
[INFO] [stderr]    Compiling itertools v0.10.5
[INFO] [stderr]    Compiling petgraph v0.6.4
[INFO] [stderr]    Compiling enum-map v1.1.1
[INFO] [stderr]    Compiling bit-set v0.5.3
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]    Compiling bio-types v1.0.1
[INFO] [stderr]    Compiling simba v0.6.0
[INFO] [stderr]    Compiling fxhash v0.2.1
[INFO] [stderr]    Compiling ndarray v0.15.6
[INFO] [stderr]    Compiling itertools-num v0.1.3
[INFO] [stderr]    Compiling ordered-float v3.9.2
[INFO] [stderr]    Compiling strum_macros v0.24.3
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[INFO] [stderr]    Compiling safemem v0.3.3
[INFO] [stderr]    Compiling serde v1.0.196
[INFO] [stderr]    Compiling triple_accel v0.4.0
[INFO] [stderr]    Compiling strum v0.24.1
[INFO] [stderr]    Compiling bytecount v0.6.7
[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling buffer-redux v1.0.0
[INFO] [stderr]    Compiling capwriter v0.2.0
[INFO] [stderr]    Compiling num-iter v0.1.44
[INFO] [stderr]    Compiling scoped_threadpool v0.1.9
[INFO] [stderr]    Compiling zerocopy v0.7.32
[INFO] [stderr]    Compiling once_cell v1.19.0
[INFO] [stderr]    Compiling num v0.4.1
[INFO] [stderr]    Compiling vec_map v0.8.2
[INFO] [stderr]    Compiling multimap v0.8.3
[INFO] [stderr]    Compiling csv v1.3.0
[INFO] [stderr]    Compiling serde_json v1.0.113
[INFO] [stderr]    Compiling seq_io v0.3.2
[INFO] [stderr]    Compiling nalgebra v0.29.0
[INFO] [stderr]    Compiling statrs v0.16.0
[INFO] [stderr]    Compiling bio v1.3.0
[INFO] [stderr]    Compiling lt-fm-index v0.7.0-alpha.2
[INFO] [stderr]    Compiling sigalign v0.3.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 18.95s
[INFO] running `Command { std: "docker" "inspect" "2ca5d863e22878d0febd2830cc88fe78a6a7415dbf526eb06653665964bc6e67", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "2ca5d863e22878d0febd2830cc88fe78a6a7415dbf526eb06653665964bc6e67", kill_on_drop: false }`
[INFO] [stdout] 2ca5d863e22878d0febd2830cc88fe78a6a7415dbf526eb06653665964bc6e67
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-02-10" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 4d196f0455cbfdf469f8195721467a455114e44a2f743f599b476da9156c4d08
[INFO] running `Command { std: "docker" "start" "-a" "4d196f0455cbfdf469f8195721467a455114e44a2f743f599b476da9156c4d08", kill_on_drop: false }`
[INFO] [stderr]    Compiling sigalign v0.3.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 1.17s
[INFO] running `Command { std: "docker" "inspect" "4d196f0455cbfdf469f8195721467a455114e44a2f743f599b476da9156c4d08", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "4d196f0455cbfdf469f8195721467a455114e44a2f743f599b476da9156c4d08", kill_on_drop: false }`
[INFO] [stdout] 4d196f0455cbfdf469f8195721467a455114e44a2f743f599b476da9156c4d08
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-02-10" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] 441ab78082be811286215d97ad26408e246b7f88923d8012864ea0226b06ac6a
[INFO] running `Command { std: "docker" "start" "-a" "441ab78082be811286215d97ad26408e246b7f88923d8012864ea0226b06ac6a", kill_on_drop: false }`
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 0.05s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/sigalign-a4a903d72110d159)
[INFO] [stdout] 
[INFO] [stdout] running 3 tests
[INFO] [stdout] test algorithm::wave_front::fill::tests::test_if_the_default_value_of_component_is_filled_with_zero ... ok
[INFO] [stdout] test aligner::regulator::tests::test_gcd_calculation_for_penalties ... ok
[INFO] [stdout] test utils::file_reader::tests::test_reading_fasta_from_bytes ... 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] [stderr]    Doc-tests sigalign
[INFO] [stdout] 
[INFO] [stdout] running 9 tests
[INFO] [stdout] test src/aligner/mod.rs - aligner (line 78) ... FAILED
[INFO] [stdout] test src/reference/mod.rs - reference (line 75) ... FAILED
[INFO] [stdout] test src/aligner/mod.rs - aligner (line 66) ... FAILED
[INFO] [stdout] test src/reference/mod.rs - reference (line 61) ... FAILED
[INFO] [stdout] test src/reference/mod.rs - reference (line 90) ... FAILED
[INFO] [stdout] test src/aligner/mod.rs - aligner (line 89) ... FAILED
[INFO] [stdout] test src/lib.rs - (line 7) ... FAILED
[INFO] [stdout] test src/reference/mod.rs - reference (line 98) ... FAILED
[INFO] [stdout] test src/reference/mod.rs - reference (line 29) ... ok
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout] 
[INFO] [stdout] ---- src/aligner/mod.rs - aligner (line 78) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:79:27
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut sequence_buffer = reference.get_sequence_buffer();
[INFO] [stdout]   |                           ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:81:5
[INFO] [stdout]   |
[INFO] [stdout] 5 |     aligner.alignment(
[INFO] [stdout]   |     ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:82:10
[INFO] [stdout]   |
[INFO] [stdout] 6 |         &reference,
[INFO] [stdout]   |          ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/reference/mod.rs - reference (line 75) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:76:27
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut sequence_buffer = reference.get_sequence_buffer();
[INFO] [stdout]   |                           ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:78:5
[INFO] [stdout]   |
[INFO] [stdout] 5 |     aligner.alignment(
[INFO] [stdout]   |     ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:79:10
[INFO] [stdout]   |
[INFO] [stdout] 6 |         &reference,
[INFO] [stdout]   |          ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/aligner/mod.rs - aligner (line 66) stdout ----
[INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Aligner`
[INFO] [stdout]  --> src/aligner/mod.rs:67:19
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut aligner = Aligner::<LocalMode, LinearStrategy>::new(
[INFO] [stdout]   |                   ^^^^^^^ use of undeclared type `Aligner`
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::aligner::Aligner;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `LocalMode` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:67:29
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut aligner = Aligner::<LocalMode, LinearStrategy>::new(
[INFO] [stdout]   |                             ^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::aligner::mode::LocalMode;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `LinearStrategy` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:67:40
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut aligner = Aligner::<LocalMode, LinearStrategy>::new(
[INFO] [stdout]   |                                        ^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::aligner::allocation_strategy::LinearStrategy;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0412, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0412`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/reference/mod.rs - reference (line 61) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:62:14
[INFO] [stdout]   |
[INFO] [stdout] 3 | let result = aligner.align_query(
[INFO] [stdout]   |              ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:63:6
[INFO] [stdout]   |
[INFO] [stdout] 4 |     &reference,
[INFO] [stdout]   |      ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:67:14
[INFO] [stdout]   |
[INFO] [stdout] 8 | let result = aligner.align_fasta_file(
[INFO] [stdout]   |              ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:68:6
[INFO] [stdout]   |
[INFO] [stdout] 9 |     &reference,
[INFO] [stdout]   |      ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 4 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/reference/mod.rs - reference (line 90) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:91:21
[INFO] [stdout]   |
[INFO] [stdout] 3 | let mut reference = reference;
[INFO] [stdout]   |                     ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/aligner/mod.rs - aligner (line 89) stdout ----
[INFO] [stdout] error[E0412]: cannot find type `AlignmentResult` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:90:13
[INFO] [stdout]   |
[INFO] [stdout] 3 | let result: AlignmentResult = aligner.align_query(
[INFO] [stdout]   |             ^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::results::AlignmentResult;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:90:31
[INFO] [stdout]   |
[INFO] [stdout] 3 | let result: AlignmentResult = aligner.align_query(
[INFO] [stdout]   |                               ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:91:6
[INFO] [stdout]   |
[INFO] [stdout] 4 |     &reference,
[INFO] [stdout]   |      ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `FastaAlignmentResult` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:94:13
[INFO] [stdout]   |
[INFO] [stdout] 7 | let result: FastaAlignmentResult = aligner.align_fasta_file(
[INFO] [stdout]   |             ^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::results::fasta::FastaAlignmentResult;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `aligner` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:94:36
[INFO] [stdout]   |
[INFO] [stdout] 7 | let result: FastaAlignmentResult = aligner.align_fasta_file(
[INFO] [stdout]   |                                    ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/aligner/mod.rs:95:6
[INFO] [stdout]   |
[INFO] [stdout] 8 |     &reference,
[INFO] [stdout]   |      ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 6 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0412, E0425.
[INFO] [stdout] For more information about an error, try `rustc --explain E0412`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/lib.rs - (line 7) stdout ----
[INFO] [stdout] error[E0599]: no method named `unwrap` found for struct `AlignmentResult` in the current scope
[INFO] [stdout]   --> src/lib.rs:33:53
[INFO] [stdout]    |
[INFO] [stdout] 29 | let result = aligner.align_query(&reference, query).unwrap();
[INFO] [stdout]    |                                                     ^^^^^^ method not found in `AlignmentResult`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0599`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/reference/mod.rs - reference (line 98) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `reference` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:102:1
[INFO] [stdout]   |
[INFO] [stdout] 7 | reference.save_to(&mut buffer).unwrap();
[INFO] [stdout]   | ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `buffer` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:102:24
[INFO] [stdout]   |
[INFO] [stdout] 7 | reference.save_to(&mut buffer).unwrap();
[INFO] [stdout]   |                        ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Reference`
[INFO] [stdout]  --> src/reference/mod.rs:104:17
[INFO] [stdout]   |
[INFO] [stdout] 9 | let reference = Reference::<Lfi32B2V64, InMemoryStorage>::load_from(&buffer[..]).unwrap();
[INFO] [stdout]   |                 ^^^^^^^^^ use of undeclared type `Reference`
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::reference::Reference;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `Lfi32B2V64` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:104:29
[INFO] [stdout]   |
[INFO] [stdout] 9 | let reference = Reference::<Lfi32B2V64, InMemoryStorage>::load_from(&buffer[..]).unwrap();
[INFO] [stdout]   |                             ^^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this type alias
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::reference::pattern_index::lfi::Lfi32B2V64;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `InMemoryStorage` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:104:41
[INFO] [stdout]   |
[INFO] [stdout] 9 | let reference = Reference::<Lfi32B2V64, InMemoryStorage>::load_from(&buffer[..]).unwrap();
[INFO] [stdout]   |                                         ^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]   |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]   |
[INFO] [stdout] 2 + use sigalign::reference::sequence_storage::in_memory::InMemoryStorage;
[INFO] [stdout]   |
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `buffer` in this scope
[INFO] [stdout]  --> src/reference/mod.rs:104:70
[INFO] [stdout]   |
[INFO] [stdout] 9 | let reference = Reference::<Lfi32B2V64, InMemoryStorage>::load_from(&buffer[..]).unwrap();
[INFO] [stdout]   |                                                                      ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 6 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0412, E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0412`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout]     src/aligner/mod.rs - aligner (line 66)
[INFO] [stdout]     src/aligner/mod.rs - aligner (line 78)
[INFO] [stdout]     src/aligner/mod.rs - aligner (line 89)
[INFO] [stdout]     src/lib.rs - (line 7)
[INFO] [stdout]     src/reference/mod.rs - reference (line 61)
[INFO] [stdout]     src/reference/mod.rs - reference (line 75)
[INFO] [stdout]     src/reference/mod.rs - reference (line 90)
[INFO] [stdout]     src/reference/mod.rs - reference (line 98)
[INFO] [stdout] 
[INFO] [stdout] test result: FAILED. 1 passed; 8 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.75s
[INFO] [stdout] 
[INFO] [stderr] error: doctest failed, to rerun pass `--doc`
[INFO] running `Command { std: "docker" "inspect" "441ab78082be811286215d97ad26408e246b7f88923d8012864ea0226b06ac6a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "441ab78082be811286215d97ad26408e246b7f88923d8012864ea0226b06ac6a", kill_on_drop: false }`
[INFO] [stdout] 441ab78082be811286215d97ad26408e246b7f88923d8012864ea0226b06ac6a
