[INFO] fetching crate bio_edit 0.1.1...
[INFO] testing bio_edit-0.1.1 against beta-2026-03-05 for beta-1.95-1
[INFO] extracting crate bio_edit 0.1.1 into /workspace/builds/worker-6-tc2/source
[INFO] started tweaking crates.io crate bio_edit 0.1.1
[INFO] finished tweaking crates.io crate bio_edit 0.1.1
[INFO] tweaked toml for crates.io crate bio_edit 0.1.1 written to /workspace/builds/worker-6-tc2/source/Cargo.toml
[INFO] validating manifest of crates.io crate bio_edit 0.1.1 on toolchain beta-2026-03-05
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2026-03-05" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2026-03-05" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]      Locking 21 packages to latest compatible versions
[INFO] [stderr]       Adding bio-types v0.12.1 (available: v1.0.4)
[INFO] [stderr]       Adding bit-set v0.5.3 (available: v0.9.0)
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2026-03-05" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2026-03-05" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 632f6386c4a7d3f6b59b93c457eb4ed6e1e69bdf79a5034934aa2ef16bf3e87f
[INFO] running `Command { std: "docker" "start" "-a" "632f6386c4a7d3f6b59b93c457eb4ed6e1e69bdf79a5034934aa2ef16bf3e87f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "632f6386c4a7d3f6b59b93c457eb4ed6e1e69bdf79a5034934aa2ef16bf3e87f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "632f6386c4a7d3f6b59b93c457eb4ed6e1e69bdf79a5034934aa2ef16bf3e87f", kill_on_drop: false }`
[INFO] [stdout] 632f6386c4a7d3f6b59b93c457eb4ed6e1e69bdf79a5034934aa2ef16bf3e87f
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2026-03-05" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 451c4905755f3816e20f44ba0b34cba59c42f15fe2b47e944792cf12ec426436
[INFO] running `Command { std: "docker" "start" "-a" "451c4905755f3816e20f44ba0b34cba59c42f15fe2b47e944792cf12ec426436", kill_on_drop: false }`
[INFO] [stderr]    Compiling bit-vec v0.6.3
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling bit-set v0.5.3
[INFO] [stderr]    Compiling strum_macros v0.23.1
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling bio-types v0.12.1
[INFO] [stderr]    Compiling bio_edit v0.1.1 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 6.18s
[INFO] running `Command { std: "docker" "inspect" "451c4905755f3816e20f44ba0b34cba59c42f15fe2b47e944792cf12ec426436", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "451c4905755f3816e20f44ba0b34cba59c42f15fe2b47e944792cf12ec426436", kill_on_drop: false }`
[INFO] [stdout] 451c4905755f3816e20f44ba0b34cba59c42f15fe2b47e944792cf12ec426436
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2026-03-05" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] a4d5bafd3c9133b97293b5eb8507aa5c1faa5a31dbe1996dab1606b64900edfc
[INFO] running `Command { std: "docker" "start" "-a" "a4d5bafd3c9133b97293b5eb8507aa5c1faa5a31dbe1996dab1606b64900edfc", kill_on_drop: false }`
[INFO] [stderr]    Compiling bio_edit v0.1.1 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.49s
[INFO] running `Command { std: "docker" "inspect" "a4d5bafd3c9133b97293b5eb8507aa5c1faa5a31dbe1996dab1606b64900edfc", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a4d5bafd3c9133b97293b5eb8507aa5c1faa5a31dbe1996dab1606b64900edfc", kill_on_drop: false }`
[INFO] [stdout] a4d5bafd3c9133b97293b5eb8507aa5c1faa5a31dbe1996dab1606b64900edfc
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2026-03-05" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] d9a00f19b175d0a7562011f9e93e758a6a1cf7e8604f6c9c6405f7e403779630
[INFO] running `Command { std: "docker" "start" "-a" "d9a00f19b175d0a7562011f9e93e758a6a1cf7e8604f6c9c6405f7e403779630", 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/bio_edit-92718641318ce59c)
[INFO] [stdout] 
[INFO] [stderr]    Doc-tests bio_edit
[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] [stdout] 
[INFO] [stdout] running 10 tests
[INFO] [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise::Aligner (line 402) ... ignored
[INFO] [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise::Aligner (line 407) ... ignored
[INFO] [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise::Aligner (line 414) ... ignored
[INFO] [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::yclip_suffix (line 384) ... FAILED
[INFO] [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::xclip_prefix (line 303) ... FAILED
[INFO] [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::yclip (line 343) ... FAILED
[INFO] [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::xclip_suffix (line 323) ... FAILED
[INFO] [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::yclip_prefix (line 364) ... FAILED
[INFO] [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::xclip (line 281) ... FAILED
[INFO] [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise (line 13) ... FAILED
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout] 
[INFO] [stdout] ---- src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::yclip_suffix (line 384) stdout ----
[INFO] [stdout] error[E0433]: cannot find module or crate `bio` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:385:5
[INFO] [stdout]     |
[INFO] [stdout] 385 | use bio::alignment::pairwise::{Scoring, MIN_SCORE};
[INFO] [stdout]     |     ^^^ use of unresolved module or unlinked crate `bio`
[INFO] [stdout]     |
[INFO] [stdout]     = help: if you wanted to use a crate named `bio`, use `cargo add bio` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::xclip_prefix (line 303) stdout ----
[INFO] [stdout] error[E0433]: cannot find module or crate `bio` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:304:5
[INFO] [stdout]     |
[INFO] [stdout] 304 | use bio::alignment::pairwise::{Scoring, MIN_SCORE};
[INFO] [stdout]     |     ^^^ use of unresolved module or unlinked crate `bio`
[INFO] [stdout]     |
[INFO] [stdout]     = help: if you wanted to use a crate named `bio`, use `cargo add bio` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::yclip (line 343) stdout ----
[INFO] [stdout] error[E0433]: cannot find module or crate `bio` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:344:5
[INFO] [stdout]     |
[INFO] [stdout] 344 | use bio::alignment::pairwise::{Scoring, MIN_SCORE};
[INFO] [stdout]     |     ^^^ use of unresolved module or unlinked crate `bio`
[INFO] [stdout]     |
[INFO] [stdout]     = help: if you wanted to use a crate named `bio`, use `cargo add bio` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::xclip_suffix (line 323) stdout ----
[INFO] [stdout] error[E0433]: cannot find module or crate `bio` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:324:5
[INFO] [stdout]     |
[INFO] [stdout] 324 | use bio::alignment::pairwise::{Scoring, MIN_SCORE};
[INFO] [stdout]     |     ^^^ use of unresolved module or unlinked crate `bio`
[INFO] [stdout]     |
[INFO] [stdout]     = help: if you wanted to use a crate named `bio`, use `cargo add bio` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::yclip_prefix (line 364) stdout ----
[INFO] [stdout] error[E0433]: cannot find module or crate `bio` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:365:5
[INFO] [stdout]     |
[INFO] [stdout] 365 | use bio::alignment::pairwise::{Scoring, MIN_SCORE};
[INFO] [stdout]     |     ^^^ use of unresolved module or unlinked crate `bio`
[INFO] [stdout]     |
[INFO] [stdout]     = help: if you wanted to use a crate named `bio`, use `cargo add bio` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::xclip (line 281) stdout ----
[INFO] [stdout] error[E0433]: cannot find module or crate `bio` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:282:5
[INFO] [stdout]     |
[INFO] [stdout] 282 | use bio::alignment::pairwise::{Scoring, MIN_SCORE};
[INFO] [stdout]     |     ^^^ use of unresolved module or unlinked crate `bio`
[INFO] [stdout]     |
[INFO] [stdout]     = help: if you wanted to use a crate named `bio`, use `cargo add bio` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/alignment/pairwise/mod.rs - alignment::pairwise (line 13) stdout ----
[INFO] [stdout] error[E0433]: cannot find module or crate `bio` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:14:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | use bio::alignment::pairwise::*;
[INFO] [stdout]    |     ^^^ use of unresolved module or unlinked crate `bio`
[INFO] [stdout]    |
[INFO] [stdout]    = help: if you wanted to use a crate named `bio`, use `cargo add bio` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find module or crate `bio` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:15:5
[INFO] [stdout]    |
[INFO] [stdout] 15 | use bio::alignment::AlignmentOperation::*;
[INFO] [stdout]    |     ^^^ use of unresolved module or unlinked crate `bio`
[INFO] [stdout]    |
[INFO] [stdout]    = help: if you wanted to use a crate named `bio`, use `cargo add bio` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved imports `bio::alignment::pairwise::*`, `bio::alignment::AlignmentOperation::*`
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:14:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | use bio::alignment::pairwise::*;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 15 | use bio::alignment::AlignmentOperation::*;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:28:6
[INFO] [stdout]    |
[INFO] [stdout] 28 |     [Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |      ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:28:13
[INFO] [stdout]    |
[INFO] [stdout] 28 |     [Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:28:20
[INFO] [stdout]    |
[INFO] [stdout] 28 |     [Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                    ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:28:27
[INFO] [stdout]    |
[INFO] [stdout] 28 |     [Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                           ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:28:34
[INFO] [stdout]    |
[INFO] [stdout] 28 |     [Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                  ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Subst` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:28:41
[INFO] [stdout]    |
[INFO] [stdout] 28 |     [Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:28:48
[INFO] [stdout]    |
[INFO] [stdout] 28 |     [Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                                ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:28:55
[INFO] [stdout]    |
[INFO] [stdout] 28 |     [Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                                       ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:28:62
[INFO] [stdout]    |
[INFO] [stdout] 28 |     [Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                                              ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `MIN_SCORE` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:50:12
[INFO] [stdout]    |
[INFO] [stdout] 50 |     .xclip(MIN_SCORE) // Clipping penalty for x set to 'negative infinity', hence global in x
[INFO] [stdout]    |            ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:61:9
[INFO] [stdout]    |
[INFO] [stdout] 61 |         Match,
[INFO] [stdout]    |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:62:9
[INFO] [stdout]    |
[INFO] [stdout] 62 |         Match,
[INFO] [stdout]    |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:63:9
[INFO] [stdout]    |
[INFO] [stdout] 63 |         Match,
[INFO] [stdout]    |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:64:9
[INFO] [stdout]    |
[INFO] [stdout] 64 |         Match,
[INFO] [stdout]    |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:65:9
[INFO] [stdout]    |
[INFO] [stdout] 65 |         Match,
[INFO] [stdout]    |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Subst` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:66:9
[INFO] [stdout]    |
[INFO] [stdout] 66 |         Subst,
[INFO] [stdout]    |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:67:9
[INFO] [stdout]    |
[INFO] [stdout] 67 |         Match,
[INFO] [stdout]    |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:68:9
[INFO] [stdout]    |
[INFO] [stdout] 68 |         Match,
[INFO] [stdout]    |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:69:9
[INFO] [stdout]    |
[INFO] [stdout] 69 |         Match
[INFO] [stdout]    |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `MIN_SCORE` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:76:12
[INFO] [stdout]    |
[INFO] [stdout] 76 |     .xclip(MIN_SCORE) // Clipping penalty for x set to 'negative infinity', hence global in x
[INFO] [stdout]    |            ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `MIN_SCORE` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:77:12
[INFO] [stdout]    |
[INFO] [stdout] 77 |     .yclip(MIN_SCORE); // Clipping penalty for y set to 'negative infinity', hence global in y
[INFO] [stdout]    |            ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Del` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:6
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |      ^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Del` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:11
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |           ^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Del` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:16
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                ^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Del` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:21
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                     ^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:26
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                          ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:33
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                 ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:40
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                        ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:47
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                               ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:54
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                                      ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Subst` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:61
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:68
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                                                    ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:75
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                                                           ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:85:82
[INFO] [stdout]    |
[INFO] [stdout] 85 |     [Del, Del, Del, Del, Match, Match, Match, Match, Match, Subst, Match, Match, Match]
[INFO] [stdout]    |                                                                                  ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0422]: cannot find struct, variant or union type `Scoring` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:98:15
[INFO] [stdout]    |
[INFO] [stdout] 98 | let scoring = Scoring {
[INFO] [stdout]    |               ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]   --> /rustc/ad726b5063362ec9897ef3d67452fc5606ee70fa/library/alloc/src/string.rs:353:0
[INFO] [stdout]    |
[INFO] [stdout]    = note: similarly named struct `String` defined here
[INFO] [stdout] help: a struct with a similar name exists
[INFO] [stdout]    |
[INFO] [stdout] 98 - let scoring = Scoring {
[INFO] [stdout] 98 + let scoring = String {
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `MIN_SCORE` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:104:19
[INFO] [stdout]     |
[INFO] [stdout] 104 |     xclip_suffix: MIN_SCORE,
[INFO] [stdout]     |                   ^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:119:9
[INFO] [stdout]     |
[INFO] [stdout] 119 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:120:9
[INFO] [stdout]     |
[INFO] [stdout] 120 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:121:9
[INFO] [stdout]     |
[INFO] [stdout] 121 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:122:9
[INFO] [stdout]     |
[INFO] [stdout] 122 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:123:9
[INFO] [stdout]     |
[INFO] [stdout] 123 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:124:9
[INFO] [stdout]     |
[INFO] [stdout] 124 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:125:9
[INFO] [stdout]     |
[INFO] [stdout] 125 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:126:9
[INFO] [stdout]     |
[INFO] [stdout] 126 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:127:9
[INFO] [stdout]     |
[INFO] [stdout] 127 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:128:9
[INFO] [stdout]     |
[INFO] [stdout] 128 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:129:9
[INFO] [stdout]     |
[INFO] [stdout] 129 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `Match` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:130:9
[INFO] [stdout]     |
[INFO] [stdout] 130 |         Match,
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Aligner` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:21:19
[INFO] [stdout]    |
[INFO] [stdout] 21 | let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, &score);
[INFO] [stdout]    |                   ^^^^^^^ use of undeclared type `Aligner`
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Aligner` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:34:19
[INFO] [stdout]    |
[INFO] [stdout] 34 | let mut aligner = Aligner::new(-5, -1, &score);
[INFO] [stdout]    |                   ^^^^^^^ use of undeclared type `Aligner`
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Scoring` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:49:15
[INFO] [stdout]    |
[INFO] [stdout] 49 | let scoring = Scoring::new(-5, -1, &score) // Gap open, gap extend and match score function
[INFO] [stdout]    |               ^^^^^^^ use of undeclared type `Scoring`
[INFO] [stdout]    |
[INFO] [stdout] help: a struct with a similar name exists
[INFO] [stdout]    |
[INFO] [stdout] 49 - let scoring = Scoring::new(-5, -1, &score) // Gap open, gap extend and match score function
[INFO] [stdout] 49 + let scoring = String::new(-5, -1, &score) // Gap open, gap extend and match score function
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Aligner` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:52:19
[INFO] [stdout]    |
[INFO] [stdout] 52 | let mut aligner = Aligner::with_scoring(scoring);
[INFO] [stdout]    |                   ^^^^^^^ use of undeclared type `Aligner`
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `Yclip` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:60:9
[INFO] [stdout]    |
[INFO] [stdout] 60 |         Yclip(4),
[INFO] [stdout]    |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Scoring` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:75:15
[INFO] [stdout]    |
[INFO] [stdout] 75 | let scoring = Scoring::from_scores(-5, -1, 1, -1) // Gap open, extend, match, mismatch score
[INFO] [stdout]    |               ^^^^^^^ use of undeclared type `Scoring`
[INFO] [stdout]    |
[INFO] [stdout] help: a struct with a similar name exists
[INFO] [stdout]    |
[INFO] [stdout] 75 - let scoring = Scoring::from_scores(-5, -1, 1, -1) // Gap open, extend, match, mismatch score
[INFO] [stdout] 75 + let scoring = String::from_scores(-5, -1, 1, -1) // Gap open, extend, match, mismatch score
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Aligner` in this scope
[INFO] [stdout]   --> src/alignment/pairwise/mod.rs:78:19
[INFO] [stdout]    |
[INFO] [stdout] 78 | let mut aligner = Aligner::with_scoring(scoring);
[INFO] [stdout]    |                   ^^^^^^^ use of undeclared type `Aligner`
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Aligner` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:110:19
[INFO] [stdout]     |
[INFO] [stdout] 110 | let mut aligner = Aligner::with_capacity_and_scoring(x.len(), y.len(), scoring);
[INFO] [stdout]     |                   ^^^^^^^ use of undeclared type `Aligner`
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `Yclip` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:117:9
[INFO] [stdout]     |
[INFO] [stdout] 117 |         Yclip(4),
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `Xclip` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:118:9
[INFO] [stdout]     |
[INFO] [stdout] 118 |         Xclip(6),
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `Yclip` in this scope
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:131:9
[INFO] [stdout]     |
[INFO] [stdout] 131 |         Yclip(4)
[INFO] [stdout]     |         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 62 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0422, E0425, E0432, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0422`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout]     src/alignment/pairwise/mod.rs - alignment::pairwise (line 13)
[INFO] [stdout]     src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::xclip (line 281)
[INFO] [stdout]     src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::xclip_prefix (line 303)
[INFO] [stdout]     src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::xclip_suffix (line 323)
[INFO] [stdout]     src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::yclip (line 343)
[INFO] [stdout]     src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::yclip_prefix (line 364)
[INFO] [stdout]     src/alignment/pairwise/mod.rs - alignment::pairwise::Scoring<F>::yclip_suffix (line 384)
[INFO] [stdout] 
[INFO] [stdout] test result: FAILED. 0 passed; 7 failed; 3 ignored; 0 measured; 0 filtered out; finished in 0.33s
[INFO] [stdout] 
[INFO] [stderr] error: doctest failed, to rerun pass `--doc`
[INFO] running `Command { std: "docker" "inspect" "d9a00f19b175d0a7562011f9e93e758a6a1cf7e8604f6c9c6405f7e403779630", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d9a00f19b175d0a7562011f9e93e758a6a1cf7e8604f6c9c6405f7e403779630", kill_on_drop: false }`
[INFO] [stdout] d9a00f19b175d0a7562011f9e93e758a6a1cf7e8604f6c9c6405f7e403779630
