[INFO] fetching crate rvdna 0.1.0... [INFO] checking rvdna-0.1.0 against master#3f6250a7bb79e600d9036bbc7c8f65af43933643 for pr-147859 [INFO] extracting crate rvdna 0.1.0 into /workspace/builds/worker-5-tc1/source [INFO] started tweaking crates.io crate rvdna 0.1.0 [INFO] removed 0 missing tests [INFO] finished tweaking crates.io crate rvdna 0.1.0 [INFO] tweaked toml for crates.io crate rvdna 0.1.0 written to /workspace/builds/worker-5-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate rvdna 0.1.0 on toolchain 3f6250a7bb79e600d9036bbc7c8f65af43933643 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+3f6250a7bb79e600d9036bbc7c8f65af43933643" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate rvdna 0.1.0 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" "+3f6250a7bb79e600d9036bbc7c8f65af43933643" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded lz4 v1.28.1 [INFO] [stderr] Downloaded dashmap v5.5.3 [INFO] [stderr] Downloaded memoffset v0.7.1 [INFO] [stderr] Downloaded cpu-time v1.0.0 [INFO] [stderr] Downloaded nom_locate v4.2.0 [INFO] [stderr] Downloaded pest_generator v2.8.4 [INFO] [stderr] Downloaded mmap-rs v0.6.1 [INFO] [stderr] Downloaded clap_lex v0.7.6 [INFO] [stderr] Downloaded ruvector-collections v2.0.2 [INFO] [stderr] Downloaded lru v0.12.5 [INFO] [stderr] Downloaded find-msvc-tools v0.1.5 [INFO] [stderr] Downloaded bytecount v0.6.9 [INFO] [stderr] Downloaded clap v4.5.53 [INFO] [stderr] Downloaded anndists v0.1.3 [INFO] [stderr] Downloaded ruvector-gnn v2.0.2 [INFO] [stderr] Downloaded ruvector-attention v0.1.31 [INFO] [stderr] Downloaded ruvector-core v0.1.31 [INFO] [stderr] Downloaded ruvector-dag v0.1.0 [INFO] [stderr] Downloaded clap_builder v4.5.53 [INFO] [stderr] Downloaded rkyv v0.8.12 [INFO] [stderr] Downloaded portable-atomic v1.11.1 [INFO] [stderr] Downloaded redb v2.6.3 [INFO] 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"none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:61361fe0aef631f17e9d025a70c5a647956f8c671dd02950a60ad3f5cc5526d7" "/opt/rustwide/cargo-home/bin/cargo" "+3f6250a7bb79e600d9036bbc7c8f65af43933643" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 3c4a19c92a352d5da5d266b20899e4016b284d246f9eafac70fa052cc335ba12 [INFO] running `Command { std: "docker" "start" "-a" "3c4a19c92a352d5da5d266b20899e4016b284d246f9eafac70fa052cc335ba12", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "3c4a19c92a352d5da5d266b20899e4016b284d246f9eafac70fa052cc335ba12", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "3c4a19c92a352d5da5d266b20899e4016b284d246f9eafac70fa052cc335ba12", kill_on_drop: false }` [INFO] [stdout] 3c4a19c92a352d5da5d266b20899e4016b284d246f9eafac70fa052cc335ba12 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:61361fe0aef631f17e9d025a70c5a647956f8c671dd02950a60ad3f5cc5526d7" "/opt/rustwide/cargo-home/bin/cargo" "+3f6250a7bb79e600d9036bbc7c8f65af43933643" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 29acdffd74134d7a9a1e3bdaa399db0f614d636ccbb9cfb2e52fe2464367de29 [INFO] running `Command { std: "docker" "start" "-a" "29acdffd74134d7a9a1e3bdaa399db0f614d636ccbb9cfb2e52fe2464367de29", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.103 [INFO] [stderr] Compiling quote v1.0.42 [INFO] [stderr] Compiling libc v0.2.178 [INFO] [stderr] Compiling find-msvc-tools v0.1.5 [INFO] [stderr] Checking memchr v2.7.6 [INFO] [stderr] Compiling libm v0.2.15 [INFO] [stderr] Compiling zerocopy v0.8.31 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling parking_lot_core v0.9.12 [INFO] [stderr] Compiling serde v1.0.228 [INFO] [stderr] Checking scopeguard v1.2.0 [INFO] [stderr] Checking bytes v1.11.0 [INFO] [stderr] Checking futures-core v0.3.31 [INFO] [stderr] Checking log v0.4.29 [INFO] [stderr] Checking futures-sink v0.3.31 [INFO] [stderr] Checking crossbeam-epoch v0.9.18 [INFO] [stderr] Checking lock_api v0.4.14 [INFO] [stderr] Checking regex-syntax v0.8.8 [INFO] 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Checking ruvector-gnn v2.0.2 [INFO] [stderr] Checking ruvector-collections v2.0.2 [INFO] [stderr] Checking ruvector-filter v2.0.2 [INFO] [stderr] Checking rvdna v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `QualityScore` [INFO] [stdout] --> src/rvdna.rs:40:45 [INFO] [stdout] | [INFO] [stdout] 40 | use crate::types::{DnaSequence, Nucleotide, QualityScore}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: ambiguous glob re-exports [INFO] [stdout] --> src/lib.rs:63:13 [INFO] [stdout] | [INFO] [stdout] 63 | pub use crate::kmer::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ the name `KmerIndex` in the type namespace is first re-exported here [INFO] [stdout] ... [INFO] [stdout] 66 | pub use crate::types::*; [INFO] [stdout] | --------------- but the name `KmerIndex` in the type namespace is also re-exported here [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(ambiguous_glob_reexports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `QualityScore` [INFO] [stdout] --> src/rvdna.rs:40:45 [INFO] [stdout] | [INFO] [stdout] 40 | use crate::types::{DnaSequence, Nucleotide, QualityScore}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: ambiguous glob re-exports [INFO] [stdout] --> src/lib.rs:63:13 [INFO] [stdout] | [INFO] [stdout] 63 | pub use crate::kmer::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ the name `KmerIndex` in the type namespace is first re-exported here [INFO] [stdout] ... [INFO] [stdout] 66 | pub use crate::types::*; [INFO] [stdout] | --------------- but the name `KmerIndex` in the type namespace is also re-exported here [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(ambiguous_glob_reexports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `next_ref_bases` [INFO] [stdout] --> src/variant.rs:169:9 [INFO] [stdout] | [INFO] [stdout] 169 | next_ref_bases: &[u8], [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_next_ref_bases` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `next_ref_bases` [INFO] [stdout] --> src/variant.rs:169:9 [INFO] [stdout] | [INFO] [stdout] 169 | next_ref_bases: &[u8], [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_next_ref_bases` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `hash_kmer` is never used [INFO] [stdout] --> src/kmer.rs:169:8 [INFO] [stdout] | [INFO] [stdout] 70 | impl KmerEncoder { [INFO] [stdout] | ---------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 169 | fn hash_kmer(&self, kmer: &[u8]) -> usize { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/error.rs:38:25 [INFO] [stdout] | [INFO] [stdout] 38 | DimensionMismatch { expected: usize, actual: usize }, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: the lint level is defined here [INFO] [stdout] --> src/lib.rs:16:9 [INFO] [stdout] | [INFO] [stdout] 16 | #![warn(missing_docs)] [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/error.rs:38:42 [INFO] [stdout] | [INFO] [stdout] 38 | DimensionMismatch { expected: usize, actual: usize }, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:391:9 [INFO] [stdout] | [INFO] [stdout] 391 | position: GenomicPosition, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:392:9 [INFO] [stdout] | [INFO] [stdout] 392 | quality: QualityScore, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:396:9 [INFO] [stdout] | [INFO] [stdout] 396 | position: GenomicPosition, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:397:9 [INFO] [stdout] | [INFO] [stdout] 397 | inserted_bases: DnaSequence, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:398:9 [INFO] [stdout] | [INFO] [stdout] 398 | quality: QualityScore, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:402:9 [INFO] [stdout] | [INFO] [stdout] 402 | position: GenomicPosition, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:403:9 [INFO] [stdout] | [INFO] [stdout] 403 | deleted_length: usize, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:404:9 [INFO] [stdout] | [INFO] [stdout] 404 | quality: QualityScore, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:408:9 [INFO] [stdout] | [INFO] [stdout] 408 | chromosome: u8, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:409:9 [INFO] [stdout] | [INFO] [stdout] 409 | start: u64, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:410:9 [INFO] [stdout] | [INFO] [stdout] 410 | end: u64, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:411:9 [INFO] [stdout] | [INFO] [stdout] 411 | variant_type: String, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:412:9 [INFO] [stdout] | [INFO] [stdout] 412 | quality: QualityScore, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:5 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:8 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:11 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:14 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:17 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:20 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:23 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:26 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:29 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:32 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:5 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:8 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:11 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:14 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:17 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:20 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:23 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:26 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:29 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:32 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for an enum [INFO] [stdout] --> src/kmer.rs:15:1 [INFO] [stdout] | [INFO] [stdout] 15 | pub enum KmerError { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/kmer.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | InvalidKmerLength(usize), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/kmer.rs:19:5 [INFO] [stdout] | [INFO] [stdout] 19 | InvalidSequence(String), [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/kmer.rs:21:5 [INFO] [stdout] | [INFO] [stdout] 21 | DatabaseError(#[from] ruvector_core::RuvectorError), [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/kmer.rs:23:5 [INFO] [stdout] | [INFO] [stdout] 23 | EmptySequence, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/kmer.rs:296:5 [INFO] [stdout] | [INFO] [stdout] 296 | pub id: String, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/kmer.rs:297:5 [INFO] [stdout] | [INFO] [stdout] 297 | pub score: f32, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/kmer.rs:298:5 [INFO] [stdout] | [INFO] [stdout] 298 | pub distance: f32, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `nucleotide_to_bits` is never used [INFO] [stdout] --> src/kmer.rs:30:4 [INFO] [stdout] | [INFO] [stdout] 30 | fn nucleotide_to_bits(nuc: u8) -> Option { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `hash_kmer` is never used [INFO] [stdout] --> src/kmer.rs:169:8 [INFO] [stdout] | [INFO] [stdout] 70 | impl KmerEncoder { [INFO] [stdout] | ---------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 169 | fn hash_kmer(&self, kmer: &[u8]) -> usize { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/error.rs:38:25 [INFO] [stdout] | [INFO] [stdout] 38 | DimensionMismatch { expected: usize, actual: usize }, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: the lint level is defined here [INFO] [stdout] --> src/lib.rs:16:9 [INFO] [stdout] | [INFO] [stdout] 16 | #![warn(missing_docs)] [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/error.rs:38:42 [INFO] [stdout] | [INFO] [stdout] 38 | DimensionMismatch { expected: usize, actual: usize }, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:391:9 [INFO] [stdout] | [INFO] [stdout] 391 | position: GenomicPosition, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:392:9 [INFO] [stdout] | [INFO] [stdout] 392 | quality: QualityScore, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:396:9 [INFO] [stdout] | [INFO] [stdout] 396 | position: GenomicPosition, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:397:9 [INFO] [stdout] | [INFO] [stdout] 397 | inserted_bases: DnaSequence, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:398:9 [INFO] [stdout] | [INFO] [stdout] 398 | quality: QualityScore, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:402:9 [INFO] [stdout] | [INFO] [stdout] 402 | position: GenomicPosition, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:403:9 [INFO] [stdout] | [INFO] [stdout] 403 | deleted_length: usize, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:404:9 [INFO] [stdout] | [INFO] [stdout] 404 | quality: QualityScore, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:408:9 [INFO] [stdout] | [INFO] [stdout] 408 | chromosome: u8, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:409:9 [INFO] [stdout] | [INFO] [stdout] 409 | start: u64, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:410:9 [INFO] [stdout] | [INFO] [stdout] 410 | end: u64, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:411:9 [INFO] [stdout] | [INFO] [stdout] 411 | variant_type: String, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/types.rs:412:9 [INFO] [stdout] | [INFO] [stdout] 412 | quality: QualityScore, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:5 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:8 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:11 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:14 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:17 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:20 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:23 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:26 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:29 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:447:32 [INFO] [stdout] | [INFO] [stdout] 447 | A, C, D, E, F, G, H, I, K, L, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:5 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:8 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:11 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:14 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:17 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:20 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:23 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:26 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:29 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/types.rs:448:32 [INFO] [stdout] | [INFO] [stdout] 448 | M, N, P, Q, R, S, T, V, W, Y, [INFO] [stdout] | ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for an enum [INFO] [stdout] --> src/kmer.rs:15:1 [INFO] [stdout] | [INFO] [stdout] 15 | pub enum KmerError { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/kmer.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | InvalidKmerLength(usize), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/kmer.rs:19:5 [INFO] [stdout] | [INFO] [stdout] 19 | InvalidSequence(String), [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/kmer.rs:21:5 [INFO] [stdout] | [INFO] [stdout] 21 | DatabaseError(#[from] ruvector_core::RuvectorError), [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a variant [INFO] [stdout] --> src/kmer.rs:23:5 [INFO] [stdout] | [INFO] [stdout] 23 | EmptySequence, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/kmer.rs:296:5 [INFO] [stdout] | [INFO] [stdout] 296 | pub id: String, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/kmer.rs:297:5 [INFO] [stdout] | [INFO] [stdout] 297 | pub score: f32, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: missing documentation for a struct field [INFO] [stdout] --> src/kmer.rs:298:5 [INFO] [stdout] | [INFO] [stdout] 298 | pub distance: f32, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Codec`, `KmerVectorBlock`, `RvdnaWriter`, `SparseAttention`, and `VariantTensor` [INFO] [stdout] --> src/main.rs:20:19 [INFO] [stdout] | [INFO] [stdout] 20 | rvdna::{self, Codec, KmerVectorBlock, RvdnaReader, RvdnaWriter, SparseAttention, VariantTensor}, [INFO] [stdout] | ^^^^^ ^^^^^^^^^^^^^^^ ^^^^^^^^^^^ ^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around closure body [INFO] [stdout] --> benches/dna_bench.rs:268:49 [INFO] [stdout] | [INFO] [stdout] 268 | let betas: Vec = (0..1000).map(|i| (i as f32 / 1000.0)).collect(); [INFO] [stdout] | ^ ^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 268 - let betas: Vec = (0..1000).map(|i| (i as f32 / 1000.0)).collect(); [INFO] [stdout] 268 + let betas: Vec = (0..1000).map(|i| i as f32 / 1000.0).collect(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around closure body [INFO] [stdout] --> benches/dna_bench.rs:276:49 [INFO] [stdout] | [INFO] [stdout] 276 | let betas: Vec = (0..1000).map(|i| (i as f32 / 2000.0 + 0.25)).collect(); [INFO] [stdout] | ^ ^ [INFO] [stdout] | [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 276 - let betas: Vec = (0..1000).map(|i| (i as f32 / 2000.0 + 0.25)).collect(); [INFO] [stdout] 276 + let betas: Vec = (0..1000).map(|i| i as f32 / 2000.0 + 0.25).collect(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Codec`, `KmerVectorBlock`, `RvdnaWriter`, `SparseAttention`, and `VariantTensor` [INFO] [stdout] --> src/main.rs:20:19 [INFO] [stdout] | [INFO] [stdout] 20 | rvdna::{self, Codec, KmerVectorBlock, RvdnaReader, RvdnaWriter, SparseAttention, VariantTensor}, [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: `ins_vec` [INFO] [stdout] --> src/main.rs:70:9 [INFO] [stdout] | [INFO] [stdout] 70 | let ins_vec = insulin.to_kmer_vector(11, 512)?; [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ins_vec` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ins_vec` [INFO] [stdout] --> src/main.rs:70:9 [INFO] [stdout] | [INFO] [stdout] 70 | let ins_vec = insulin.to_kmer_vector(11, 512)?; [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ins_vec` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 34s [INFO] running `Command { std: "docker" "inspect" "29acdffd74134d7a9a1e3bdaa399db0f614d636ccbb9cfb2e52fe2464367de29", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "29acdffd74134d7a9a1e3bdaa399db0f614d636ccbb9cfb2e52fe2464367de29", kill_on_drop: false }` [INFO] [stdout] 29acdffd74134d7a9a1e3bdaa399db0f614d636ccbb9cfb2e52fe2464367de29