[INFO] cloning repository https://github.com/elcharitas/bioinformatics_rs [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/elcharitas/bioinformatics_rs" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Felcharitas%2Fbioinformatics_rs", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Felcharitas%2Fbioinformatics_rs'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 6e160e7b7f4906c33a5987a3f98c24cff27a8cfe [INFO] checking elcharitas/bioinformatics_rs against try#2c4e58eac5a232e49065e517c1cf50b2715ccf85 for pr-140283 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Felcharitas%2Fbioinformatics_rs" "/workspace/builds/worker-3-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc2/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/elcharitas/bioinformatics_rs [INFO] finished tweaking git repo https://github.com/elcharitas/bioinformatics_rs [INFO] tweaked toml for git repo https://github.com/elcharitas/bioinformatics_rs written to /workspace/builds/worker-3-tc2/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/elcharitas/bioinformatics_rs on toolchain 2c4e58eac5a232e49065e517c1cf50b2715ccf85 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+2c4e58eac5a232e49065e517c1cf50b2715ccf85" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/elcharitas/bioinformatics_rs 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" "+2c4e58eac5a232e49065e517c1cf50b2715ccf85" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] warning: virtual workspace defaulting to `resolver = "1"` despite one or more workspace members being on edition 2021 which implies `resolver = "2"` [INFO] [stderr] note: to keep the current resolver, specify `workspace.resolver = "1"` in the workspace root's manifest [INFO] [stderr] note: to use the edition 2021 resolver, specify `workspace.resolver = "2"` in the workspace root's manifest [INFO] [stderr] note: for more details see https://doc.rust-lang.org/cargo/reference/resolver.html#resolver-versions [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Updating crates.io index [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded libm v0.2.14 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded statrs v0.18.0 [INFO] [stderr] Downloaded bio v2.2.0 [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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+2c4e58eac5a232e49065e517c1cf50b2715ccf85" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 6f54be8eba824d2b49520e2b18436531f4373fc526154b3fd8745f9674ff92dd [INFO] running `Command { std: "docker" "start" "-a" "6f54be8eba824d2b49520e2b18436531f4373fc526154b3fd8745f9674ff92dd", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "6f54be8eba824d2b49520e2b18436531f4373fc526154b3fd8745f9674ff92dd", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6f54be8eba824d2b49520e2b18436531f4373fc526154b3fd8745f9674ff92dd", kill_on_drop: false }` [INFO] [stdout] 6f54be8eba824d2b49520e2b18436531f4373fc526154b3fd8745f9674ff92dd [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=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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+2c4e58eac5a232e49065e517c1cf50b2715ccf85" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] d48ad3b6c9eb94709eac0712ef8b297e817aa972bd505b2e828438b28f21d276 [INFO] running `Command { std: "docker" "start" "-a" "d48ad3b6c9eb94709eac0712ef8b297e817aa972bd505b2e828438b28f21d276", kill_on_drop: false }` [INFO] [stderr] warning: virtual workspace defaulting to `resolver = "1"` despite one or more workspace members being on edition 2021 which implies `resolver = "2"` [INFO] [stderr] note: to keep the current resolver, specify `workspace.resolver = "1"` in the workspace root's manifest [INFO] [stderr] note: to use the edition 2021 resolver, specify `workspace.resolver = "2"` in the workspace root's manifest [INFO] [stderr] note: for more details see https://doc.rust-lang.org/cargo/reference/resolver.html#resolver-versions [INFO] [stderr] Compiling libm v0.2.14 [INFO] [stderr] Compiling libc v0.2.172 [INFO] [stderr] Compiling matrixmultiply v0.3.9 [INFO] [stderr] Checking bytemuck v1.23.0 [INFO] [stderr] Compiling getrandom v0.3.2 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Checking regex-automata v0.4.9 [INFO] [stderr] Compiling serde_derive v1.0.219 [INFO] [stderr] Checking hashbrown v0.15.3 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling thiserror-impl v2.0.12 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Checking csv-core v0.1.12 [INFO] [stderr] Checking fixedbitset v0.5.7 [INFO] [stderr] Checking bit-vec v0.8.0 [INFO] [stderr] Checking safe_arch v0.7.4 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking itertools v0.14.0 [INFO] [stderr] Checking bit-set v0.8.0 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking strum v0.26.3 [INFO] [stderr] Checking editdistancek v1.0.2 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Checking bytecount v0.6.8 [INFO] [stderr] Checking enum-map v2.7.3 [INFO] [stderr] Checking wide v0.7.32 [INFO] [stderr] Checking indexmap v2.9.0 [INFO] [stderr] Checking thiserror v2.0.12 [INFO] [stderr] Checking num-traits v0.2.19 [INFO] [stderr] Checking getrandom v0.2.16 [INFO] [stderr] Checking petgraph v0.7.1 [INFO] [stderr] Checking rand_core v0.6.4 [INFO] [stderr] Checking rand_core v0.9.3 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Checking rand_chacha v0.9.0 [INFO] [stderr] Checking rand v0.9.1 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Checking regex v1.11.1 [INFO] [stderr] Checking bio-types v1.0.4 [INFO] [stderr] Checking serde v1.0.219 [INFO] [stderr] Checking num-complex v0.4.6 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking ordered-float v5.0.0 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking simba v0.9.0 [INFO] [stderr] Checking num-rational v0.4.2 [INFO] [stderr] Checking ndarray v0.16.1 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking csv v1.3.1 [INFO] [stderr] Checking bv v0.11.1 [INFO] [stderr] Checking multimap v0.10.0 [INFO] [stderr] Checking nalgebra v0.33.2 [INFO] [stderr] Checking statrs v0.18.0 [INFO] [stderr] Checking bio v2.2.0 [INFO] [stderr] Checking sequence_comparison v0.1.0 (/opt/rustwide/workdir/sequence_comparison) [INFO] [stderr] Checking needleman_wunsch v0.1.0 (/opt/rustwide/workdir/needleman_wunsch) [INFO] [stderr] Checking sequence_manipulation v0.1.0 (/opt/rustwide/workdir/sequence_manipulation) [INFO] [stderr] Checking sequence_statistics v0.1.0 (/opt/rustwide/workdir/sequence_statistics) [INFO] [stderr] Checking sequence_analysis v0.1.0 (/opt/rustwide/workdir/sequence_analysis) [INFO] [stderr] Checking sequence_transformation v0.1.0 (/opt/rustwide/workdir/sequence_transformation) [INFO] [stderr] Checking smith_waterman v0.1.0 (/opt/rustwide/workdir/smith_waterman) [INFO] [stderr] Checking sequence_alignment v0.1.0 (/opt/rustwide/workdir/sequence_alignment) [INFO] [stdout] warning: unused import: `bio::alignment::pairwise::*` [INFO] [stdout] --> smith_waterman/src/lib.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use bio::alignment::pairwise::*; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seq1` [INFO] [stdout] --> smith_waterman/src/lib.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | seq1: &str, [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seq1` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seq2` [INFO] [stdout] --> smith_waterman/src/lib.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | seq2: &str, [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seq2` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `match_score` [INFO] [stdout] --> smith_waterman/src/lib.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | match_score: i32, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_match_score` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mismatch_penalty` [INFO] [stdout] --> smith_waterman/src/lib.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | mismatch_penalty: i32, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mismatch_penalty` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `gap_penalty` [INFO] [stdout] --> smith_waterman/src/lib.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | gap_penalty: i32, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_gap_penalty` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0277]: a value of type `Vec` cannot be built from an iterator over elements of type `[u8; 8]` [INFO] [stdout] --> needleman_wunsch/src/lib.rs:29:14 [INFO] [stdout] | [INFO] [stdout] 29 | .collect(), [INFO] [stdout] | ^^^^^^^ value of type `Vec` cannot be built from `std::iter::Iterator` [INFO] [stdout] | [INFO] [stdout] = help: the trait `FromIterator<[u8; 8]>` is not implemented for `Vec` [INFO] [stdout] but trait `FromIterator` is implemented for it [INFO] [stdout] = help: for that trait implementation, expected `u8`, found `[u8; 8]` [INFO] [stdout] note: the method call chain might not have had the expected associated types [INFO] [stdout] --> needleman_wunsch/src/lib.rs:28:14 [INFO] [stdout] | [INFO] [stdout] 13 | let alignment = Aligner::new(gap_penalty, mismatch_penalty, scoring.match_fn) [INFO] [stdout] | ------------------------------------------------------------- this expression has type `Aligner<{closure@lib.rs:10:63}>` [INFO] [stdout] ... [INFO] [stdout] 27 | .iter() [INFO] [stdout] | ------ `Iterator::Item` is `&(usize, usize, AlignmentOperation)` here [INFO] [stdout] 28 | .map(|(_, y, _)| y.to_le_bytes()) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ `Iterator::Item` changed to `[u8; 8]` here [INFO] [stdout] note: required by a bound in `collect` [INFO] [stdout] --> /rustc/2c4e58eac5a232e49065e517c1cf50b2715ccf85/library/core/src/iter/traits/iterator.rs:2015:5 [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0277`. [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::alignment::pairwise::*` [INFO] [stdout] --> smith_waterman/src/lib.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use bio::alignment::pairwise::*; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0277]: a value of type `Vec` cannot be built from an iterator over elements of type `[u8; 8]` [INFO] [stdout] --> needleman_wunsch/src/lib.rs:29:14 [INFO] [stdout] | [INFO] [stdout] 29 | .collect(), [INFO] [stdout] | ^^^^^^^ value of type `Vec` cannot be built from `std::iter::Iterator` [INFO] [stdout] | [INFO] [stdout] = help: the trait `FromIterator<[u8; 8]>` is not implemented for `Vec` [INFO] [stdout] but trait `FromIterator` is implemented for it [INFO] [stdout] = help: for that trait implementation, expected `u8`, found `[u8; 8]` [INFO] [stdout] note: the method call chain might not have had the expected associated types [INFO] [stdout] --> needleman_wunsch/src/lib.rs:28:14 [INFO] [stdout] | [INFO] [stdout] 13 | let alignment = Aligner::new(gap_penalty, mismatch_penalty, scoring.match_fn) [INFO] [stdout] | ------------------------------------------------------------- this expression has type `Aligner<{closure@lib.rs:10:63}>` [INFO] [stdout] ... [INFO] [stdout] 27 | .iter() [INFO] [stdout] | ------ `Iterator::Item` is `&(usize, usize, AlignmentOperation)` here [INFO] [stdout] 28 | .map(|(_, y, _)| y.to_le_bytes()) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ `Iterator::Item` changed to `[u8; 8]` here [INFO] [stdout] note: required by a bound in `collect` [INFO] [stdout] --> /rustc/2c4e58eac5a232e49065e517c1cf50b2715ccf85/library/core/src/iter/traits/iterator.rs:2015:5 [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seq1` [INFO] [stdout] --> smith_waterman/src/lib.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | seq1: &str, [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seq1` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seq2` [INFO] [stdout] --> smith_waterman/src/lib.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | seq2: &str, [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seq2` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `match_score` [INFO] [stdout] --> smith_waterman/src/lib.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | match_score: i32, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_match_score` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mismatch_penalty` [INFO] [stdout] --> smith_waterman/src/lib.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | mismatch_penalty: i32, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mismatch_penalty` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `gap_penalty` [INFO] [stdout] --> smith_waterman/src/lib.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | gap_penalty: i32, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_gap_penalty` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `needleman_wunsch` (lib) due to 1 previous error [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stdout] For more information about this error, try `rustc --explain E0277`. [INFO] [stdout] [INFO] [stderr] error: could not compile `needleman_wunsch` (lib test) due to 1 previous error [INFO] running `Command { std: "docker" "inspect" "d48ad3b6c9eb94709eac0712ef8b297e817aa972bd505b2e828438b28f21d276", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "d48ad3b6c9eb94709eac0712ef8b297e817aa972bd505b2e828438b28f21d276", kill_on_drop: false }` [INFO] [stdout] d48ad3b6c9eb94709eac0712ef8b297e817aa972bd505b2e828438b28f21d276