[INFO] fetching crate sigalign 0.3.2...
[INFO] testing sigalign-0.3.2 against 1.75.0 for beta-1.76-1
[INFO] extracting crate sigalign 0.3.2 into /workspace/builds/worker-3-tc1/source
[INFO] validating manifest of crates.io crate sigalign 0.3.2 on toolchain 1.75.0
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.75.0" "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-3-tc1/source/Cargo.toml
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.75.0" "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" "+1.75.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded seq_io v0.3.2
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded libdivsufsort-rs v0.1.2
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[INFO] [stderr]   Downloaded lt-fm-index v0.7.0-alpha.2
[INFO] [stderr]   Downloaded bio v1.3.0
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[INFO] [stderr]    Compiling sigalign v0.3.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 47.26s
[INFO] running `Command { std: "docker" "inspect" "2093f7b84912008515eb8eeb6278d8da7dadcc8a63e81972481db81b661f517a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "2093f7b84912008515eb8eeb6278d8da7dadcc8a63e81972481db81b661f517a", kill_on_drop: false }`
[INFO] [stdout] 2093f7b84912008515eb8eeb6278d8da7dadcc8a63e81972481db81b661f517a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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" "+1.75.0" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 08e1b0ce1c36d64e6d449d4a085502fcc4c3a2892dab69ea3f70df973451e3bf
[INFO] running `Command { std: "docker" "start" "-a" "08e1b0ce1c36d64e6d449d4a085502fcc4c3a2892dab69ea3f70df973451e3bf", kill_on_drop: false }`
[INFO] [stderr]    Compiling sigalign v0.3.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 3.38s
[INFO] running `Command { std: "docker" "inspect" "08e1b0ce1c36d64e6d449d4a085502fcc4c3a2892dab69ea3f70df973451e3bf", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "08e1b0ce1c36d64e6d449d4a085502fcc4c3a2892dab69ea3f70df973451e3bf", kill_on_drop: false }`
[INFO] [stdout] 08e1b0ce1c36d64e6d449d4a085502fcc4c3a2892dab69ea3f70df973451e3bf
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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" "+1.75.0" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] d113bf4296f0887fe42b03215a2a7023c144972db07a45365098e0c1ec38b25b
[INFO] running `Command { std: "docker" "start" "-a" "d113bf4296f0887fe42b03215a2a7023c144972db07a45365098e0c1ec38b25b", kill_on_drop: false }`
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 0.07s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/sigalign-3c8072f4882fd78f)
[INFO] [stdout] 
[INFO] [stdout] running 3 tests
[INFO] [stdout] test utils::file_reader::tests::test_reading_fasta_from_bytes ... ok
[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] 
[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 90) ... FAILED
[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 66) ... 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] [stderr] error: doctest failed, to rerun pass `--doc`
[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 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 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/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 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/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 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 1.38s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "d113bf4296f0887fe42b03215a2a7023c144972db07a45365098e0c1ec38b25b", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d113bf4296f0887fe42b03215a2a7023c144972db07a45365098e0c1ec38b25b", kill_on_drop: false }`
[INFO] [stdout] d113bf4296f0887fe42b03215a2a7023c144972db07a45365098e0c1ec38b25b
[INFO] testing sigalign-0.3.2 against beta-2023-12-22 for beta-1.76-1
[INFO] extracting crate sigalign 0.3.2 into /workspace/builds/worker-3-tc2/source
[INFO] validating manifest of crates.io crate sigalign 0.3.2 on toolchain beta-2023-12-22
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2023-12-22" "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-3-tc2/source/Cargo.toml
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2023-12-22" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[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-2023-12-22" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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-2023-12-22" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] a41a6ae7c5c8c4d65b51349fbd5ba7068924a10471a92612bc01ed595403b3cf
[INFO] running `Command { std: "docker" "start" "-a" "a41a6ae7c5c8c4d65b51349fbd5ba7068924a10471a92612bc01ed595403b3cf", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "a41a6ae7c5c8c4d65b51349fbd5ba7068924a10471a92612bc01ed595403b3cf", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a41a6ae7c5c8c4d65b51349fbd5ba7068924a10471a92612bc01ed595403b3cf", kill_on_drop: false }`
[INFO] [stdout] a41a6ae7c5c8c4d65b51349fbd5ba7068924a10471a92612bc01ed595403b3cf
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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-2023-12-22" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 1caf6a3220f978be9497e4fc44cdb9d7d1fbc0025153f625cc01f53ca89cbeaa
[INFO] running `Command { std: "docker" "start" "-a" "1caf6a3220f978be9497e4fc44cdb9d7d1fbc0025153f625cc01f53ca89cbeaa", kill_on_drop: false }`
[INFO] [stderr]    Compiling libm v0.2.8
[INFO] [stderr]    Compiling libc v0.2.151
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling version_check v0.9.4
[INFO] [stderr]    Compiling num-traits v0.2.17
[INFO] [stderr]    Compiling num-integer v0.1.45
[INFO] [stderr]    Compiling syn v2.0.48
[INFO] [stderr]    Compiling num-bigint v0.4.4
[INFO] [stderr]    Compiling matrixmultiply v0.3.8
[INFO] [stderr]    Compiling num-rational v0.4.1
[INFO] [stderr]    Compiling ppv-lite86 v0.2.17
[INFO] [stderr]    Compiling paste v1.0.14
[INFO] [stderr]    Compiling rustversion v1.0.14
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling getrandom v0.2.11
[INFO] [stderr]    Compiling rawpointer v0.2.1
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling typenum v1.17.0
[INFO] [stderr]    Compiling rand_core v0.6.4
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling rand v0.8.5
[INFO] [stderr]    Compiling num-complex v0.4.4
[INFO] [stderr]    Compiling approx v0.5.1
[INFO] [stderr]    Compiling cc v1.0.83
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling heck v0.4.1
[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 hashbrown v0.14.3
[INFO] [stderr]    Compiling equivalent v1.0.1
[INFO] [stderr]    Compiling byteorder v1.5.0
[INFO] [stderr]    Compiling csv-core v0.1.11
[INFO] [stderr]    Compiling num-iter v0.1.43
[INFO] [stderr]    Compiling libdivsufsort-rs v0.1.2
[INFO] [stderr]    Compiling serde_derive v1.0.194
[INFO] [stderr]    Compiling bytemuck_derive v1.5.0
[INFO] [stderr]    Compiling thiserror-impl v1.0.56
[INFO] [stderr]    Compiling strum_macros v0.25.3
[INFO] [stderr]    Compiling indexmap v2.1.0
[INFO] [stderr]    Compiling crossbeam-utils v0.8.18
[INFO] [stderr]    Compiling fixedbitset v0.4.2
[INFO] [stderr]    Compiling either v1.9.0
[INFO] [stderr]    Compiling bit-vec v0.6.3
[INFO] [stderr]    Compiling petgraph v0.6.4
[INFO] [stderr]    Compiling itertools v0.10.5
[INFO] [stderr]    Compiling bit-set v0.5.3
[INFO] [stderr]    Compiling bytemuck v1.14.0
[INFO] [stderr]    Compiling safe_arch v0.7.1
[INFO] [stderr]    Compiling thiserror v1.0.56
[INFO] [stderr]    Compiling fxhash v0.2.1
[INFO] [stderr]    Compiling ndarray v0.15.6
[INFO] [stderr]    Compiling wide v0.7.13
[INFO] [stderr]    Compiling itertools-num v0.1.3
[INFO] [stderr]    Compiling ordered-float v3.9.2
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[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling safemem v0.3.3
[INFO] [stderr]    Compiling triple_accel v0.4.0
[INFO] [stderr]    Compiling strum v0.24.1
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[INFO] [stderr]    Compiling buffer-redux v1.0.0
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[INFO] [stderr]    Compiling simba v0.6.0
[INFO] [stderr]    Compiling enum-map v1.1.1
[INFO] [stderr]    Compiling bio-types v1.0.1
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]    Compiling strum_macros v0.24.3
[INFO] [stderr]    Compiling serde v1.0.194
[INFO] [stderr]    Compiling once_cell v1.19.0
[INFO] [stderr]    Compiling scoped_threadpool v0.1.9
[INFO] [stderr]    Compiling zerocopy v0.7.32
[INFO] [stderr]    Compiling num v0.4.1
[INFO] [stderr]    Compiling multimap v0.8.3
[INFO] [stderr]    Compiling csv v1.3.0
[INFO] [stderr]    Compiling vec_map v0.8.2
[INFO] [stderr]    Compiling serde_json v1.0.111
[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 36.92s
[INFO] running `Command { std: "docker" "inspect" "1caf6a3220f978be9497e4fc44cdb9d7d1fbc0025153f625cc01f53ca89cbeaa", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "1caf6a3220f978be9497e4fc44cdb9d7d1fbc0025153f625cc01f53ca89cbeaa", kill_on_drop: false }`
[INFO] [stdout] 1caf6a3220f978be9497e4fc44cdb9d7d1fbc0025153f625cc01f53ca89cbeaa
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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-2023-12-22" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] e0865586cff5bd2da58a2bc75a7136a6e6ce9926d562631dd46aeabf90441b62
[INFO] running `Command { std: "docker" "start" "-a" "e0865586cff5bd2da58a2bc75a7136a6e6ce9926d562631dd46aeabf90441b62", kill_on_drop: false }`
[INFO] [stderr]    Compiling sigalign v0.3.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 1.89s
[INFO] running `Command { std: "docker" "inspect" "e0865586cff5bd2da58a2bc75a7136a6e6ce9926d562631dd46aeabf90441b62", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e0865586cff5bd2da58a2bc75a7136a6e6ce9926d562631dd46aeabf90441b62", kill_on_drop: false }`
[INFO] [stdout] e0865586cff5bd2da58a2bc75a7136a6e6ce9926d562631dd46aeabf90441b62
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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-2023-12-22" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] d8279ca1a1f8e8e64eb904000b0e6d07a08e9c25c95a42a9f5d80025b1b861e8
[INFO] running `Command { std: "docker" "start" "-a" "d8279ca1a1f8e8e64eb904000b0e6d07a08e9c25c95a42a9f5d80025b1b861e8", kill_on_drop: false }`
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 0.11s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/sigalign-61a58cb21589a64c)
[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 utils::file_reader::tests::test_reading_fasta_from_bytes ... ok
[INFO] [stdout] test aligner::regulator::tests::test_gcd_calculation_for_penalties ... ok
[INFO] [stderr]    Doc-tests sigalign
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 3 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 9 tests
[INFO] [stdout] test src/aligner/mod.rs - aligner (line 89) ... 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/lib.rs - (line 7) ... FAILED
[INFO] [stdout] test src/reference/mod.rs - reference (line 90) ... 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 98) ... FAILED
[INFO] [stderr] error: doctest failed, to rerun pass `--doc`
[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 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/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/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 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/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 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 1.76s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "d8279ca1a1f8e8e64eb904000b0e6d07a08e9c25c95a42a9f5d80025b1b861e8", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d8279ca1a1f8e8e64eb904000b0e6d07a08e9c25c95a42a9f5d80025b1b861e8", kill_on_drop: false }`
[INFO] [stdout] d8279ca1a1f8e8e64eb904000b0e6d07a08e9c25c95a42a9f5d80025b1b861e8
