[INFO] cloning repository https://github.com/rodtheo/bioinformatics-fundaments-in-rusts
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/rodtheo/bioinformatics-fundaments-in-rusts" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frodtheo%2Fbioinformatics-fundaments-in-rusts", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frodtheo%2Fbioinformatics-fundaments-in-rusts'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 6dbe03ceb6b7e8c7403b13d7f63b419a398cc6f7
[INFO] testing rodtheo/bioinformatics-fundaments-in-rusts against nightly-2025-01-18 for randomize-layout-2
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frodtheo%2Fbioinformatics-fundaments-in-rusts" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/rodtheo/bioinformatics-fundaments-in-rusts on toolchain nightly-2025-01-18
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+nightly-2025-01-18" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/rodtheo/bioinformatics-fundaments-in-rusts
[INFO] finished tweaking git repo https://github.com/rodtheo/bioinformatics-fundaments-in-rusts
[INFO] tweaked toml for git repo https://github.com/rodtheo/bioinformatics-fundaments-in-rusts written to /workspace/builds/worker-0-tc1/source/Cargo.toml
[INFO] crate git repo https://github.com/rodtheo/bioinformatics-fundaments-in-rusts already has a lockfile, it will not be regenerated
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+nightly-2025-01-18" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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_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@sha256:819108c5571ea2e421544af4d832f968d213c87fbe3707a016657f43d2f853bc" "/opt/rustwide/cargo-home/bin/cargo" "+nightly-2025-01-18" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 5af5f3018ae3097f8b26f5dd4b943590739c934879a40f1137e3838b070eb7bf
[INFO] running `Command { std: "docker" "start" "-a" "5af5f3018ae3097f8b26f5dd4b943590739c934879a40f1137e3838b070eb7bf", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "5af5f3018ae3097f8b26f5dd4b943590739c934879a40f1137e3838b070eb7bf", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "5af5f3018ae3097f8b26f5dd4b943590739c934879a40f1137e3838b070eb7bf", kill_on_drop: false }`
[INFO] [stdout] 5af5f3018ae3097f8b26f5dd4b943590739c934879a40f1137e3838b070eb7bf
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-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@sha256:819108c5571ea2e421544af4d832f968d213c87fbe3707a016657f43d2f853bc" "/opt/rustwide/cargo-home/bin/cargo" "+nightly-2025-01-18" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] fcbe9a30ea0c8bbbe9b86ea1646b0f4a282295df0807619785e327adc805248d
[INFO] running `Command { std: "docker" "start" "-a" "fcbe9a30ea0c8bbbe9b86ea1646b0f4a282295df0807619785e327adc805248d", kill_on_drop: false }`
[INFO] [stderr]    Compiling autocfg v1.2.0
[INFO] [stderr]    Compiling rawpointer v0.2.1
[INFO] [stderr]    Compiling lazy_static v1.4.0
[INFO] [stderr]    Compiling num-traits v0.2.18
[INFO] [stderr]    Compiling matrixmultiply v0.3.8
[INFO] [stderr]    Compiling num-complex v0.4.5
[INFO] [stderr]    Compiling num-integer v0.1.46
[INFO] [stderr]    Compiling ndarray v0.15.6
[INFO] [stderr]    Compiling globalalignment v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `globalalignment::scores::aa::blosum62`
[INFO] [stdout]  --> src/main.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use globalalignment::scores::aa::blosum62;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `io::prelude::*`
[INFO] [stdout]  --> src/main.rs:2:21
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::{cmp::max, io::prelude::*};
[INFO] [stdout]   |                     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `x`
[INFO] [stdout]    --> src/main.rs:327:21
[INFO] [stdout]     |
[INFO] [stdout] 327 |     while let Some((x, y)) = idxs {
[INFO] [stdout]     |                     ^ help: if this is intentional, prefix it with an underscore: `_x`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `y`
[INFO] [stdout]    --> src/main.rs:327:24
[INFO] [stdout]     |
[INFO] [stdout] 327 |     while let Some((x, y)) = idxs {
[INFO] [stdout]     |                        ^ help: if this is intentional, prefix it with an underscore: `_y`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 8.64s
[INFO] running `Command { std: "docker" "inspect" "fcbe9a30ea0c8bbbe9b86ea1646b0f4a282295df0807619785e327adc805248d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "fcbe9a30ea0c8bbbe9b86ea1646b0f4a282295df0807619785e327adc805248d", kill_on_drop: false }`
[INFO] [stdout] fcbe9a30ea0c8bbbe9b86ea1646b0f4a282295df0807619785e327adc805248d
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-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@sha256:819108c5571ea2e421544af4d832f968d213c87fbe3707a016657f43d2f853bc" "/opt/rustwide/cargo-home/bin/cargo" "+nightly-2025-01-18" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 53377957e5e2f36d38bf2035af783db07062ddd5cad4490bca867758f9bda0c9
[INFO] running `Command { std: "docker" "start" "-a" "53377957e5e2f36d38bf2035af783db07062ddd5cad4490bca867758f9bda0c9", kill_on_drop: false }`
[INFO] [stderr]    Compiling globalalignment v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `globalalignment::scores::aa::blosum62`
[INFO] [stdout]  --> src/main.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use globalalignment::scores::aa::blosum62;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `io::prelude::*`
[INFO] [stdout]  --> src/main.rs:2:21
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::{cmp::max, io::prelude::*};
[INFO] [stdout]   |                     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `super::*`
[INFO] [stdout]    --> src/main.rs:348:9
[INFO] [stdout]     |
[INFO] [stdout] 348 |     use super::*;
[INFO] [stdout]     |         ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `x`
[INFO] [stdout]    --> src/main.rs:327:21
[INFO] [stdout]     |
[INFO] [stdout] 327 |     while let Some((x, y)) = idxs {
[INFO] [stdout]     |                     ^ help: if this is intentional, prefix it with an underscore: `_x`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `y`
[INFO] [stdout]    --> src/main.rs:327:24
[INFO] [stdout]     |
[INFO] [stdout] 327 |     while let Some((x, y)) = idxs {
[INFO] [stdout]     |                        ^ help: if this is intentional, prefix it with an underscore: `_y`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.78s
[INFO] running `Command { std: "docker" "inspect" "53377957e5e2f36d38bf2035af783db07062ddd5cad4490bca867758f9bda0c9", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "53377957e5e2f36d38bf2035af783db07062ddd5cad4490bca867758f9bda0c9", kill_on_drop: false }`
[INFO] [stdout] 53377957e5e2f36d38bf2035af783db07062ddd5cad4490bca867758f9bda0c9
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-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@sha256:819108c5571ea2e421544af4d832f968d213c87fbe3707a016657f43d2f853bc" "/opt/rustwide/cargo-home/bin/cargo" "+nightly-2025-01-18" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] 47f208bfd5ae4397c241803a3e52107e53cdfcfb4b243fc1e8a4b7950865dced
[INFO] running `Command { std: "docker" "start" "-a" "47f208bfd5ae4397c241803a3e52107e53cdfcfb4b243fc1e8a4b7950865dced", kill_on_drop: false }`
[INFO] [stderr] warning: unused import: `globalalignment::scores::aa::blosum62`
[INFO] [stderr]  --> src/main.rs:1:5
[INFO] [stderr]   |
[INFO] [stderr] 1 | use globalalignment::scores::aa::blosum62;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `io::prelude::*`
[INFO] [stderr]  --> src/main.rs:2:21
[INFO] [stderr]   |
[INFO] [stderr] 2 | use std::{cmp::max, io::prelude::*};
[INFO] [stderr]   |                     ^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `super::*`
[INFO] [stderr]    --> src/main.rs:348:9
[INFO] [stderr]     |
[INFO] [stderr] 348 |     use super::*;
[INFO] [stderr]     |         ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `x`
[INFO] [stderr]    --> src/main.rs:327:21
[INFO] [stderr]     |
[INFO] [stderr] 327 |     while let Some((x, y)) = idxs {
[INFO] [stderr]     |                     ^ help: if this is intentional, prefix it with an underscore: `_x`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `y`
[INFO] [stderr]    --> src/main.rs:327:24
[INFO] [stderr]     |
[INFO] [stderr] 327 |     while let Some((x, y)) = idxs {
[INFO] [stderr]     |                        ^ help: if this is intentional, prefix it with an underscore: `_y`
[INFO] [stderr] 
[INFO] [stderr] warning: `globalalignment` (bin "globalalignment" test) generated 5 warnings (run `cargo fix --bin "globalalignment" --tests` to apply 3 suggestions)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.02s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/globalalignment-75b5fe87d30f8d52)
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/globalalignment-ed88c23604a3fb3d)
[INFO] [stdout] test scores::aa::tests::test_blosum62 ... ok
[INFO] [stderr]    Doc-tests globalalignment
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stdout] test src/scores/aa.rs - scores::aa::blosum62 (line 87) ... FAILED
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout] 
[INFO] [stdout] ---- src/scores/aa.rs - scores::aa::blosum62 (line 87) stdout ----
[INFO] [stdout] error[E0433]: failed to resolve: use of undeclared crate or module `bio`
[INFO] [stdout]  --> src/scores/aa.rs:88:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use bio::scores::blosum62;
[INFO] [stdout]   |     ^^^ use of undeclared crate or module `bio`
[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] 
[INFO] [stdout] failures:
[INFO] [stdout]     src/scores/aa.rs - scores::aa::blosum62 (line 87)
[INFO] [stdout] 
[INFO] [stdout] test result: FAILED. 0 passed; 1 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.11s
[INFO] [stdout] 
[INFO] [stderr] error: doctest failed, to rerun pass `--doc`
[INFO] running `Command { std: "docker" "inspect" "47f208bfd5ae4397c241803a3e52107e53cdfcfb4b243fc1e8a4b7950865dced", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "47f208bfd5ae4397c241803a3e52107e53cdfcfb4b243fc1e8a4b7950865dced", kill_on_drop: false }`
[INFO] [stdout] 47f208bfd5ae4397c241803a3e52107e53cdfcfb4b243fc1e8a4b7950865dced
