[INFO] fetching crate redicat 0.4.2... [INFO] linting redicat-0.4.2 against nightly for clippy-nonminimal_bool-denied [INFO] extracting crate redicat 0.4.2 into /workspace/builds/worker-1-tc1/source [INFO] started tweaking crates.io crate redicat 0.4.2 [INFO] finished tweaking crates.io crate redicat 0.4.2 [INFO] tweaked toml for crates.io crate redicat 0.4.2 written to /workspace/builds/worker-1-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate redicat 0.4.2 on toolchain nightly [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+nightly" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate redicat 0.4.2 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" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded lru_time_cache v0.11.11 [INFO] [stderr] Downloaded hdf5-metno-derive v0.9.3 [INFO] [stderr] Downloaded hdf5-metno-types v0.9.0 [INFO] [stderr] Downloaded anndata-hdf5 v0.5.0 [INFO] [stderr] Downloaded hdf5-metno-sys v0.9.1 [INFO] [stderr] Downloaded anndata v0.6.1 [INFO] [stderr] Downloaded polars-expr v0.45.1 [INFO] [stderr] Downloaded nalgebra-sparse v0.10.0 [INFO] [stderr] Downloaded hdf5-metno v0.9.2 [INFO] [stderr] Downloaded libdeflate-sys v0.7.5 [INFO] [stderr] Downloaded polars v0.45.1 [INFO] [stderr] Downloaded polars-io v0.45.1 [INFO] [stderr] Downloaded bio v0.41.0 [INFO] [stderr] Downloaded simd-json v0.14.3 [INFO] [stderr] Downloaded sqlparser v0.52.0 [INFO] [stderr] Downloaded polars-parquet v0.45.1 [INFO] [stderr] Downloaded sysinfo v0.32.1 [INFO] [stderr] Downloaded polars-ops v0.45.1 [INFO] [stderr] Downloaded polars-arrow v0.45.1 [INFO] [stderr] Downloaded polars-plan v0.45.1 [INFO] [stderr] Downloaded polars-stream v0.45.1 [INFO] [stderr] Downloaded rust-htslib v0.50.0 [INFO] [stderr] Downloaded polars-pipe v0.45.1 [INFO] [stderr] Downloaded polars-core v0.45.1 [INFO] [stderr] Downloaded polars-lazy v0.45.1 [INFO] [stderr] Downloaded polars-sql v0.45.1 [INFO] [stderr] Downloaded polars-compute v0.45.1 [INFO] [stderr] Downloaded polars-time v0.45.1 [INFO] [stderr] Downloaded polars-utils v0.45.1 [INFO] [stderr] Downloaded flume v0.10.14 [INFO] [stderr] Downloaded polars-mem-engine v0.45.1 [INFO] [stderr] Downloaded polars-json v0.45.1 [INFO] [stderr] Downloaded polars-row v0.45.1 [INFO] [stderr] Downloaded libdeflater v0.7.5 [INFO] [stderr] Downloaded halfbrown v0.2.5 [INFO] [stderr] Downloaded value-trait v0.10.1 [INFO] [stderr] Downloaded enum-map-derive v0.6.0 [INFO] [stderr] Downloaded enum-map v1.1.1 [INFO] [stderr] Downloaded strum_macros v0.23.1 [INFO] [stderr] Downloaded grep-cli v0.1.12 [INFO] [stderr] Downloaded debug_unsafe v0.1.4 [INFO] [stderr] Downloaded polars-schema v0.45.1 [INFO] [stderr] Downloaded polars-error v0.45.1 [INFO] [stderr] Downloaded strum v0.23.0 [INFO] [stderr] Downloaded core_affinity v0.5.10 [INFO] [stderr] Downloaded rust-lapper v1.2.0 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded rstest v0.11.0 [INFO] [stderr] Downloaded curl-sys v0.4.85+curl-8.18.0 [INFO] [stderr] Downloaded gzp v0.10.1 [INFO] [stderr] Downloaded hdf5-metno-src v0.9.5 [INFO] [stderr] Downloaded hts-sys v2.2.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+nightly" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 4a2a9cd8457bd418b99ebffa843b976bd3a0b15a062c07cb08ae9b49c7c747f8 [INFO] running `Command { std: "docker" "start" "-a" "4a2a9cd8457bd418b99ebffa843b976bd3a0b15a062c07cb08ae9b49c7c747f8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "4a2a9cd8457bd418b99ebffa843b976bd3a0b15a062c07cb08ae9b49c7c747f8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "4a2a9cd8457bd418b99ebffa843b976bd3a0b15a062c07cb08ae9b49c7c747f8", kill_on_drop: false }` [INFO] [stdout] 4a2a9cd8457bd418b99ebffa843b976bd3a0b15a062c07cb08ae9b49c7c747f8 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+nightly" "clippy" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] b2b867a1605a85ac5724d044d9628870e46fbae4fa0a3502c165c2a3f3fde1d1 [INFO] running `Command { std: "docker" "start" "-a" "b2b867a1605a85ac5724d044d9628870e46fbae4fa0a3502c165c2a3f3fde1d1", kill_on_drop: false }` [INFO] [stderr] Compiling syn v2.0.115 [INFO] [stderr] Compiling zerocopy v0.8.39 [INFO] [stderr] Compiling cmake v0.1.57 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Checking aho-corasick v1.1.4 [INFO] [stderr] Checking getrandom v0.2.17 [INFO] [stderr] Compiling object v0.37.3 [INFO] [stderr] Compiling matrixmultiply v0.3.10 [INFO] [stderr] Checking rand_core v0.6.4 [INFO] [stderr] Checking parking_lot_core v0.9.12 [INFO] [stderr] Compiling stacker v0.1.23 [INFO] [stderr] Checking indexmap v2.13.0 [INFO] [stderr] Compiling polars-utils v0.45.1 [INFO] [stderr] Checking parking_lot v0.12.5 [INFO] [stderr] Compiling rustix v1.1.3 [INFO] [stderr] Compiling libz-sys v1.1.23 [INFO] [stderr] Checking chrono v0.4.43 [INFO] [stderr] Checking memmap2 v0.9.9 [INFO] [stderr] Compiling polars-schema v0.45.1 [INFO] [stderr] Checking regex-automata v0.4.14 [INFO] [stderr] Compiling polars-arrow v0.45.1 [INFO] [stderr] Checking chrono-tz v0.10.4 [INFO] [stderr] Checking atoi v2.0.0 [INFO] [stderr] Compiling polars-compute v0.45.1 [INFO] [stderr] Compiling regex-syntax v0.8.9 [INFO] [stderr] Checking debug_unsafe v0.1.4 [INFO] [stderr] Checking itoap v1.0.1 [INFO] [stderr] Checking atoi_simd v0.16.1 [INFO] [stderr] Compiling zstd-sys v2.0.16+zstd.1.5.7 [INFO] [stderr] Checking regex v1.12.3 [INFO] [stderr] Compiling libz-ng-sys v1.1.23 [INFO] [stderr] Compiling ar_archive_writer v0.5.1 [INFO] [stderr] Checking crossterm v0.29.0 [INFO] [stderr] Checking ndarray v0.16.1 [INFO] [stderr] Compiling psm v0.1.30 [INFO] [stderr] Compiling synstructure v0.13.2 [INFO] [stderr] Compiling multiversion-macros v0.7.4 [INFO] [stderr] Compiling lz4-sys v1.11.1+lz4-1.10.0 [INFO] [stderr] Compiling polars-core v0.45.1 [INFO] [stderr] Compiling serde_derive v1.0.228 [INFO] [stderr] Compiling zerocopy-derive v0.8.39 [INFO] [stderr] Compiling bytemuck_derive v1.10.2 [INFO] [stderr] Compiling thiserror-impl v2.0.18 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Checking bytemuck v1.25.0 [INFO] [stderr] Checking multiversion v0.7.4 [INFO] [stderr] Compiling zerofrom-derive v0.1.6 [INFO] [stderr] Checking thiserror v2.0.18 [INFO] [stderr] Compiling yoke-derive v0.8.1 [INFO] [stderr] Checking zerofrom v0.1.6 [INFO] [stderr] Compiling zerovec-derive v0.11.2 [INFO] [stderr] Checking comfy-table v7.2.2 [INFO] [stderr] Compiling displaydoc v0.2.5 [INFO] [stderr] Checking yoke v0.8.1 [INFO] [stderr] Checking serde v1.0.228 [INFO] [stderr] Compiling polars-ops v0.45.1 [INFO] [stderr] Compiling snap v1.1.1 [INFO] [stderr] Checking brotli-decompressor v4.0.3 [INFO] [stderr] Checking argminmax v0.6.3 [INFO] [stderr] Checking polars-arrow-format v0.1.0 [INFO] [stderr] Checking compact_str v0.8.1 [INFO] [stderr] 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polars v0.45.1 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling hdf5-metno-types v0.9.0 [INFO] [stderr] Checking nalgebra v0.33.2 [INFO] [stderr] Checking idna_adapter v1.2.1 [INFO] [stderr] Compiling proc-macro-crate v3.4.0 [INFO] [stderr] Compiling hts-sys v2.2.0 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Checking simba v0.5.1 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling pin-project-internal v1.1.10 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking num_cpus v1.17.0 [INFO] [stderr] Compiling hdf5-metno v0.9.2 [INFO] [stderr] Checking clap_builder v4.5.58 [INFO] [stderr] Checking idna v1.1.0 [INFO] [stderr] Checking pin-project v1.1.10 [INFO] [stderr] Checking tempfile v3.25.0 [INFO] [stderr] Checking bio-types v1.0.4 [INFO] [stderr] Compiling hdf5-metno-derive v0.9.3 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Checking form_urlencoded v1.2.2 [INFO] [stderr] Compiling clap_derive v4.5.55 [INFO] [stderr] Compiling enum-map-derive v0.6.0 [INFO] [stderr] Checking bstr v1.12.1 [INFO] [stderr] Checking nanorand v0.7.0 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Checking bit-vec v0.6.3 [INFO] [stderr] Checking permutation v0.4.1 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking clap v2.34.0 [INFO] [stderr] Checking flume v0.10.14 [INFO] [stderr] Checking nalgebra v0.27.1 [INFO] [stderr] Checking petgraph v0.6.5 [INFO] [stderr] Checking clap v4.5.58 [INFO] [stderr] Checking bit-set v0.5.3 [INFO] [stderr] Checking globset v0.4.18 [INFO] [stderr] Checking csv v1.4.0 [INFO] [stderr] Checking alga v0.9.3 [INFO] [stderr] Checking enum-map v1.1.1 [INFO] [stderr] Checking polars-time v0.45.1 [INFO] [stderr] Checking nalgebra-sparse v0.10.0 [INFO] [stderr] Checking url v2.5.8 [INFO] [stderr] Checking bv v0.11.1 [INFO] [stderr] Checking libdeflater v0.7.5 [INFO] [stderr] Compiling structopt-derive v0.4.18 [INFO] [stderr] Checking core_affinity v0.5.10 [INFO] [stderr] Compiling strum_macros v0.23.1 [INFO] [stderr] Checking polars-io v0.45.1 [INFO] [stderr] Compiling getset v0.1.6 [INFO] [stderr] Checking half v2.7.1 [INFO] [stderr] Checking multimap v0.8.3 [INFO] [stderr] Compiling derive-new v0.7.0 [INFO] [stderr] Checking ndarray v0.15.6 [INFO] [stderr] Checking ndarray v0.17.2 [INFO] [stderr] Checking crossbeam-queue v0.3.12 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking ordered-float v1.1.1 [INFO] [stderr] Checking bytecount v0.6.9 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking strum v0.23.0 [INFO] [stderr] Checking ciborium-ll v0.2.2 [INFO] [stderr] Checking env_logger v0.9.3 [INFO] [stderr] Checking crossbeam v0.8.4 [INFO] [stderr] Checking structopt v0.3.26 [INFO] [stderr] Checking gzp v0.10.1 [INFO] [stderr] Checking grep-cli v0.1.12 [INFO] [stderr] Compiling rstest v0.11.0 [INFO] [stderr] Checking smartstring v0.2.10 [INFO] [stderr] Checking rust-lapper v1.2.0 [INFO] [stderr] Checking wait-timeout v0.2.1 [INFO] [stderr] Checking lru_time_cache v0.11.11 [INFO] [stderr] Checking rusty-fork v0.3.1 [INFO] [stderr] Checking criterion-plot v0.6.0 [INFO] [stderr] Checking bit-set v0.8.0 [INFO] [stderr] Checking plotters v0.3.7 [INFO] [stderr] Checking ciborium v0.2.2 [INFO] [stderr] Checking rand v0.9.2 [INFO] [stderr] Checking rand_xorshift v0.4.0 [INFO] [stderr] Checking sprs v0.11.4 [INFO] [stderr] Checking rand_chacha v0.9.0 [INFO] [stderr] Checking tinytemplate v1.2.1 [INFO] [stderr] Checking unarray v0.1.4 [INFO] [stderr] Checking proptest v1.10.0 [INFO] [stderr] Checking statrs v0.15.0 [INFO] [stderr] Checking criterion v0.7.0 [INFO] [stderr] Checking polars-expr v0.45.1 [INFO] [stderr] Checking bio v0.41.0 [INFO] [stderr] Checking polars-mem-engine v0.45.1 [INFO] [stderr] Checking anndata v0.6.1 [INFO] [stderr] Checking anndata-hdf5 v0.5.0 [INFO] [stderr] Checking rust-htslib v0.50.0 [INFO] [stderr] Checking redicat v0.4.2 (/opt/rustwide/workdir) [INFO] [stdout] warning: manual slice size calculation [INFO] [stdout] --> src/lib/core/sparse.rs:431:17 [INFO] [stdout] | [INFO] [stdout] 431 | values.len() * std::mem::size_of::(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `std::mem::size_of_val(values)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_slice_size_calculation [INFO] [stdout] = note: `#[warn(clippy::manual_slice_size_calculation)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: manual slice size calculation [INFO] [stdout] --> src/lib/core/sparse.rs:478:9 [INFO] [stdout] | [INFO] [stdout] 478 | row_offsets.len() * std::mem::size_of::() [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `std::mem::size_of_val(row_offsets)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_slice_size_calculation [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: manual slice size calculation [INFO] [stdout] --> src/lib/core/sparse.rs:479:15 [INFO] [stdout] | [INFO] [stdout] 479 | + col_indices.len() * std::mem::size_of::() [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `std::mem::size_of_val(col_indices)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_slice_size_calculation [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: manual slice size calculation [INFO] [stdout] --> src/lib/core/sparse.rs:480:15 [INFO] [stdout] | [INFO] [stdout] 480 | + values.len() * std::mem::size_of::() [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `std::mem::size_of_val(values)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_slice_size_calculation [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/engine/par_granges/intervals.rs:130:60 [INFO] [stdout] | [INFO] [stdout] 130 | for (i, (a_lapper, b_lapper)) in a_ivs.into_iter().zip(b_ivs.into_iter()).enumerate() { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> /rustc/3645249d79dfb136b5d8de3ce153d19d6698d92d/library/core/src/iter/traits/iterator.rs:629:11 [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] = note: `#[warn(clippy::useless_conversion)]` on by default [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 130 - for (i, (a_lapper, b_lapper)) in a_ivs.into_iter().zip(b_ivs.into_iter()).enumerate() { [INFO] [stdout] 130 + for (i, (a_lapper, b_lapper)) in a_ivs.into_iter().zip(b_ivs).enumerate() { [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/engine/par_granges/intervals.rs:131:51 [INFO] [stdout] | [INFO] [stdout] 131 | intervals[i] = a_lapper.into_iter().chain(b_lapper.into_iter()).collect(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> /rustc/3645249d79dfb136b5d8de3ce153d19d6698d92d/library/core/src/iter/traits/iterator.rs:510:11 [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 131 - intervals[i] = a_lapper.into_iter().chain(b_lapper.into_iter()).collect(); [INFO] [stdout] 131 + intervals[i] = a_lapper.into_iter().chain(b_lapper).collect(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: manual implementation of `.is_multiple_of()` [INFO] [stdout] --> src/lib/engine/par_granges/scheduler.rs:293:53 [INFO] [stdout] | [INFO] [stdout] 293 | if completed == total_chunks || completed % log_step == 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace with: `completed.is_multiple_of(log_step)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_is_multiple_of [INFO] [stdout] = note: `#[warn(clippy::manual_is_multiple_of)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:123:32 [INFO] [stdout] | [INFO] [stdout] 123 | self.convert_streaming(data.to_vec().into_iter(), output_path) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:103:12 [INFO] [stdout] | [INFO] [stdout] 103 | I: IntoIterator, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 123 - self.convert_streaming(data.to_vec().into_iter(), output_path) [INFO] [stdout] 123 + self.convert_streaming(data.to_vec(), output_path) [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary use of `to_vec` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:123:32 [INFO] [stdout] | [INFO] [stdout] 123 | self.convert_streaming(data.to_vec().into_iter(), output_path) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `data.iter().cloned()` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_to_owned [INFO] [stdout] = note: `#[warn(clippy::unnecessary_to_owned)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:270:56 [INFO] [stdout] | [INFO] [stdout] 270 | for (name, matrix) in forward_names.iter().zip(forward_layers.into_iter()) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> /rustc/3645249d79dfb136b5d8de3ce153d19d6698d92d/library/core/src/iter/traits/iterator.rs:629:11 [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 270 - for (name, matrix) in forward_names.iter().zip(forward_layers.into_iter()) { [INFO] [stdout] 270 + for (name, matrix) in forward_names.iter().zip(forward_layers) { [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: deref which would be done by auto-deref [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:271:32 [INFO] [stdout] | [INFO] [stdout] 271 | adata.layers().add(*name, matrix)?; [INFO] [stdout] | ^^^^^ help: try: `name` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_auto_deref [INFO] [stdout] = note: `#[warn(clippy::explicit_auto_deref)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:276:60 [INFO] [stdout] | [INFO] [stdout] 276 | for (name, matrix) in reverse_names.iter().zip(reverse_layers.into_iter()) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> /rustc/3645249d79dfb136b5d8de3ce153d19d6698d92d/library/core/src/iter/traits/iterator.rs:629:11 [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 276 - for (name, matrix) in reverse_names.iter().zip(reverse_layers.into_iter()) { [INFO] [stdout] 276 + for (name, matrix) in reverse_names.iter().zip(reverse_layers) { [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: deref which would be done by auto-deref [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:277:36 [INFO] [stdout] | [INFO] [stdout] 277 | adata.layers().add(*name, matrix)?; [INFO] [stdout] | ^^^^^ help: try: `name` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_auto_deref [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: redundant closure [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:983:13 [INFO] [stdout] | [INFO] [stdout] 983 | || FxHashSet::default(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: replace the closure with the associated function itself: `FxHashSet::default` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure [INFO] [stdout] = note: `#[warn(clippy::redundant_closure)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: redundant closure [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:976:13 [INFO] [stdout] | [INFO] [stdout] 976 | || FxHashSet::default(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: replace the closure with the associated function itself: `FxHashSet::default` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:985:29 [INFO] [stdout] | [INFO] [stdout] 985 | left.extend(right.into_iter()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> /rustc/3645249d79dfb136b5d8de3ce153d19d6698d92d/library/core/src/iter/traits/collect.rs:416:17 [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 985 - left.extend(right.into_iter()); [INFO] [stdout] 985 + left.extend(right); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: very complex type used. Consider factoring parts into `type` definitions [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1167:10 [INFO] [stdout] | [INFO] [stdout] 1167 | ) -> Result<(Vec>, Vec>)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#type_complexity [INFO] [stdout] = note: `#[warn(clippy::type_complexity)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: casting to the same type is unnecessary (`u32` -> `u32`) [INFO] [stdout] --> src/lib/pipeline/bam2mtx/processor.rs:270:16 [INFO] [stdout] | [INFO] [stdout] 270 | if (pileup.depth() as u32) >= self.config.max_depth { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: try: `pileup.depth()` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast [INFO] [stdout] = note: `#[warn(clippy::unnecessary_cast)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: redundant closure [INFO] [stdout] --> src/lib/pipeline/call/anndata_ops.rs:106:18 [INFO] [stdout] | [INFO] [stdout] 106 | .map(|m| SparseOps::estimate_csr_bytes(m)) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace the closure with the associated function itself: `SparseOps::estimate_csr_bytes` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: redundant closure [INFO] [stdout] --> src/lib/pipeline/call/anndata_ops.rs:123:30 [INFO] [stdout] | [INFO] [stdout] 123 | .map_err(|e| RedicatError::Io(e))?, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: replace the closure with the tuple variant itself: `RedicatError::Io` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: using `contains()` instead of `iter().any()` is more efficient [INFO] [stdout] --> src/lib/pipeline/call/anndata_ops.rs:174:38 [INFO] [stdout] | [INFO] [stdout] 174 | .filter(|(name, _)| !keep.iter().any(|&k| k == name.as_str())) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `keep.contains(&name.as_str())` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_contains [INFO] [stdout] = note: `#[warn(clippy::manual_contains)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: very complex type used. Consider factoring parts into `type` definitions [INFO] [stdout] --> src/lib/pipeline/call/editing_analysis.rs:170:6 [INFO] [stdout] | [INFO] [stdout] 170 | ) -> ( [INFO] [stdout] | ______^ [INFO] [stdout] 171 | | HashMap>, [INFO] [stdout] 172 | | HashMap>, [INFO] [stdout] 173 | | HashMap>, [INFO] [stdout] 174 | | ) { [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#type_complexity [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this function has too many arguments (8/7) [INFO] [stdout] --> src/lib/pipeline/call/editing_analysis.rs:408:1 [INFO] [stdout] | [INFO] [stdout] 408 | / pub fn annotate_variants_pipeline( [INFO] [stdout] 409 | | adata: AnnDataContainer, [INFO] [stdout] 410 | | editing_sites: Arc>, [INFO] [stdout] 411 | | reference: Arc, [INFO] [stdout] ... | [INFO] [stdout] 416 | | min_coverage: u32, [INFO] [stdout] 417 | | ) -> Result { [INFO] [stdout] | |_____________________________^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#too_many_arguments [INFO] [stdout] = note: `#[warn(clippy::too_many_arguments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this function has too many arguments (12/7) [INFO] [stdout] --> src/lib/pipeline/call/editing_analysis.rs:768:1 [INFO] [stdout] | [INFO] [stdout] 768 | / fn classify_mismatch_fast( [INFO] [stdout] 769 | | site_idx: usize, [INFO] [stdout] 770 | | coverage_slice: &[u32], [INFO] [stdout] 771 | | ref_strings: &[String], [INFO] [stdout] ... | [INFO] [stdout] 780 | | min_coverage: u32, [INFO] [stdout] 781 | | ) -> MismatchClassification { [INFO] [stdout] | |___________________________^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#too_many_arguments [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: digits grouped inconsistently by underscores [INFO] [stdout] --> src/commands/bam2mtx/args.rs:114:36 [INFO] [stdout] | [INFO] [stdout] 114 | assert_eq!(args.max_depth, 655_36); [INFO] [stdout] | ^^^^^^ help: consider: `65_536` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#inconsistent_digit_grouping [INFO] [stdout] = note: `#[warn(clippy::inconsistent_digit_grouping)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: manual slice size calculation [INFO] [stdout] --> src/lib/core/sparse.rs:431:17 [INFO] [stdout] | [INFO] [stdout] 431 | values.len() * std::mem::size_of::(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `std::mem::size_of_val(values)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_slice_size_calculation [INFO] [stdout] = note: `#[warn(clippy::manual_slice_size_calculation)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: manual slice size calculation [INFO] [stdout] --> src/lib/core/sparse.rs:478:9 [INFO] [stdout] | [INFO] [stdout] 478 | row_offsets.len() * std::mem::size_of::() [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `std::mem::size_of_val(row_offsets)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_slice_size_calculation [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: manual slice size calculation [INFO] [stdout] --> src/lib/core/sparse.rs:479:15 [INFO] [stdout] | [INFO] [stdout] 479 | + col_indices.len() * std::mem::size_of::() [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `std::mem::size_of_val(col_indices)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_slice_size_calculation [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: manual slice size calculation [INFO] [stdout] --> src/lib/core/sparse.rs:480:15 [INFO] [stdout] | [INFO] [stdout] 480 | + values.len() * std::mem::size_of::() [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `std::mem::size_of_val(values)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_slice_size_calculation [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: casting to the same type is unnecessary (`u32` -> `u32`) [INFO] [stdout] --> src/commands/bam2mtx/engine.rs:186:25 [INFO] [stdout] | [INFO] [stdout] 186 | let depth = pileup.depth() as u32; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ help: try: `pileup.depth()` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast [INFO] [stdout] = note: `#[warn(clippy::unnecessary_cast)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: you seem to be trying to move all elements into a new `HashMap` [INFO] [stdout] --> src/commands/bam2mtx/engine.rs:269:25 [INFO] [stdout] | [INFO] [stdout] 269 | counts: counts.drain().collect(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ help: consider using `mem::take`: `std::mem::take(&mut counts)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#drain_collect [INFO] [stdout] = note: `#[warn(clippy::drain_collect)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: manual checked division [INFO] [stdout] --> src/commands/bam2mtx/input.rs:243:31 [INFO] [stdout] | [INFO] [stdout] 243 | let estimated_chunks = if hotspot_limit == 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ check performed here [INFO] [stdout] ... [INFO] [stdout] 246 | positions.len().saturating_add(hotspot_limit - 1) / hotspot_limit [INFO] [stdout] | ----------------------------------------------------------------- division performed here [INFO] [stdout] | [INFO] [stdout] = help: consider using `checked_div` [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_checked_ops [INFO] [stdout] = note: `#[warn(clippy::manual_checked_ops)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: casting to the same type is unnecessary (`usize` -> `usize`) [INFO] [stdout] --> src/commands/bam2mtx/mod.rs:79:29 [INFO] [stdout] | [INFO] [stdout] 79 | triplet_spill_nnz: (chunk_size as usize * 16).max(500_000), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: try: `chunk_size` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/engine/par_granges/intervals.rs:130:60 [INFO] [stdout] | [INFO] [stdout] 130 | for (i, (a_lapper, b_lapper)) in a_ivs.into_iter().zip(b_ivs.into_iter()).enumerate() { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> /rustc/3645249d79dfb136b5d8de3ce153d19d6698d92d/library/core/src/iter/traits/iterator.rs:629:11 [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] = note: `#[warn(clippy::useless_conversion)]` on by default [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 130 - for (i, (a_lapper, b_lapper)) in a_ivs.into_iter().zip(b_ivs.into_iter()).enumerate() { [INFO] [stdout] 130 + for (i, (a_lapper, b_lapper)) in a_ivs.into_iter().zip(b_ivs).enumerate() { [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/engine/par_granges/intervals.rs:131:51 [INFO] [stdout] | [INFO] [stdout] 131 | intervals[i] = a_lapper.into_iter().chain(b_lapper.into_iter()).collect(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> /rustc/3645249d79dfb136b5d8de3ce153d19d6698d92d/library/core/src/iter/traits/iterator.rs:510:11 [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 131 - intervals[i] = a_lapper.into_iter().chain(b_lapper.into_iter()).collect(); [INFO] [stdout] 131 + intervals[i] = a_lapper.into_iter().chain(b_lapper).collect(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: manual implementation of `.is_multiple_of()` [INFO] [stdout] --> src/lib/engine/par_granges/scheduler.rs:293:53 [INFO] [stdout] | [INFO] [stdout] 293 | if completed == total_chunks || completed % log_step == 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace with: `completed.is_multiple_of(log_step)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_is_multiple_of [INFO] [stdout] = note: `#[warn(clippy::manual_is_multiple_of)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: very complex type used. Consider factoring parts into `type` definitions [INFO] [stdout] --> src/lib/engine/par_granges/scheduler.rs:387:10 [INFO] [stdout] | [INFO] [stdout] 387 | ) -> impl Strategy>, u64, u64)>> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#type_complexity [INFO] [stdout] = note: `#[warn(clippy::type_complexity)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the borrowed expression implements the required traits [INFO] [stdout] --> src/lib/engine/par_granges/scheduler.rs:408:41 [INFO] [stdout] | [INFO] [stdout] 408 | chr_rec.push_tag(b"SN", &i.to_string()); [INFO] [stdout] | ^^^^^^^^^^^^^^ help: change this to: `i.to_string()` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrows_for_generic_args [INFO] [stdout] = note: `#[warn(clippy::needless_borrows_for_generic_args)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the borrowed expression implements the required traits [INFO] [stdout] --> src/lib/engine/par_granges/scheduler.rs:409:41 [INFO] [stdout] | [INFO] [stdout] 409 | chr_rec.push_tag(b"LN", &chr.2.to_string()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ help: change this to: `chr.2.to_string()` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrows_for_generic_args [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this boolean expression can be simplified [INFO] [stdout] --> src/lib/engine/position/pileup_position.rs:276:20 [INFO] [stdout] | [INFO] [stdout] 276 | if !(position.pos == site_pos - 1) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `(position.pos != site_pos - 1)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#nonminimal_bool [INFO] [stdout] = note: `#[warn(clippy::nonminimal_bool)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:123:32 [INFO] [stdout] | [INFO] [stdout] 123 | self.convert_streaming(data.to_vec().into_iter(), output_path) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:103:12 [INFO] [stdout] | [INFO] [stdout] 103 | I: IntoIterator, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 123 - self.convert_streaming(data.to_vec().into_iter(), output_path) [INFO] [stdout] 123 + self.convert_streaming(data.to_vec(), output_path) [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary use of `to_vec` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:123:32 [INFO] [stdout] | [INFO] [stdout] 123 | self.convert_streaming(data.to_vec().into_iter(), output_path) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `data.iter().cloned()` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_to_owned [INFO] [stdout] = note: `#[warn(clippy::unnecessary_to_owned)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:270:56 [INFO] [stdout] | [INFO] [stdout] 270 | for (name, matrix) in forward_names.iter().zip(forward_layers.into_iter()) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> /rustc/3645249d79dfb136b5d8de3ce153d19d6698d92d/library/core/src/iter/traits/iterator.rs:629:11 [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 270 - for (name, matrix) in forward_names.iter().zip(forward_layers.into_iter()) { [INFO] [stdout] 270 + for (name, matrix) in forward_names.iter().zip(forward_layers) { [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: deref which would be done by auto-deref [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:271:32 [INFO] [stdout] | [INFO] [stdout] 271 | adata.layers().add(*name, matrix)?; [INFO] [stdout] | ^^^^^ help: try: `name` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_auto_deref [INFO] [stdout] = note: `#[warn(clippy::explicit_auto_deref)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:276:60 [INFO] [stdout] | [INFO] [stdout] 276 | for (name, matrix) in reverse_names.iter().zip(reverse_layers.into_iter()) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> /rustc/3645249d79dfb136b5d8de3ce153d19d6698d92d/library/core/src/iter/traits/iterator.rs:629:11 [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 276 - for (name, matrix) in reverse_names.iter().zip(reverse_layers.into_iter()) { [INFO] [stdout] 276 + for (name, matrix) in reverse_names.iter().zip(reverse_layers) { [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: deref which would be done by auto-deref [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:277:36 [INFO] [stdout] | [INFO] [stdout] 277 | adata.layers().add(*name, matrix)?; [INFO] [stdout] | ^^^^^ help: try: `name` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_auto_deref [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: casting to the same type is unnecessary (`u32` -> `u32`) [INFO] [stdout] --> src/commands/bam2mtx/engine.rs:186:25 [INFO] [stdout] | [INFO] [stdout] 186 | let depth = pileup.depth() as u32; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ help: try: `pileup.depth()` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast [INFO] [stdout] = note: `#[warn(clippy::unnecessary_cast)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: you seem to be trying to move all elements into a new `HashMap` [INFO] [stdout] --> src/commands/bam2mtx/engine.rs:269:25 [INFO] [stdout] | [INFO] [stdout] 269 | counts: counts.drain().collect(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ help: consider using `mem::take`: `std::mem::take(&mut counts)` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#drain_collect [INFO] [stdout] = note: `#[warn(clippy::drain_collect)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: redundant closure [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:983:13 [INFO] [stdout] | [INFO] [stdout] 983 | || FxHashSet::default(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: replace the closure with the associated function itself: `FxHashSet::default` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure [INFO] [stdout] = note: `#[warn(clippy::redundant_closure)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: redundant closure [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:976:13 [INFO] [stdout] | [INFO] [stdout] 976 | || FxHashSet::default(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: replace the closure with the associated function itself: `FxHashSet::default` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: explicit call to `.into_iter()` in function argument accepting `IntoIterator` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:985:29 [INFO] [stdout] | [INFO] [stdout] 985 | left.extend(right.into_iter()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: this parameter accepts any `IntoIterator`, so you don't need to call `.into_iter()` [INFO] [stdout] --> /rustc/3645249d79dfb136b5d8de3ce153d19d6698d92d/library/core/src/iter/traits/collect.rs:416:17 [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_conversion [INFO] [stdout] help: consider removing the `.into_iter()` [INFO] [stdout] | [INFO] [stdout] 985 - left.extend(right.into_iter()); [INFO] [stdout] 985 + left.extend(right); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: manual checked division [INFO] [stdout] --> src/commands/bam2mtx/input.rs:243:31 [INFO] [stdout] | [INFO] [stdout] 243 | let estimated_chunks = if hotspot_limit == 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ check performed here [INFO] [stdout] ... [INFO] [stdout] 246 | positions.len().saturating_add(hotspot_limit - 1) / hotspot_limit [INFO] [stdout] | ----------------------------------------------------------------- division performed here [INFO] [stdout] | [INFO] [stdout] = help: consider using `checked_div` [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_checked_ops [INFO] [stdout] = note: `#[warn(clippy::manual_checked_ops)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: very complex type used. Consider factoring parts into `type` definitions [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1167:10 [INFO] [stdout] | [INFO] [stdout] 1167 | ) -> Result<(Vec>, Vec>)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#type_complexity [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field assignment outside of initializer for an instance created with Default::default() [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1351:9 [INFO] [stdout] | [INFO] [stdout] 1351 | config.stranded = true; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: consider initializing the variable with `pipeline::bam2mtx::anndata_output::AnnDataConfig { stranded: true, threads: 2, chunk_size: 4, batch_size: 4, triplet_spill_nnz: 2, ..Default::default() }` and removing relevant reassignments [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1350:9 [INFO] [stdout] | [INFO] [stdout] 1350 | let mut config = AnnDataConfig::default(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#field_reassign_with_default [INFO] [stdout] = note: `#[warn(clippy::field_reassign_with_default)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field assignment outside of initializer for an instance created with Default::default() [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1431:9 [INFO] [stdout] | [INFO] [stdout] 1431 | config.stranded = true; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: consider initializing the variable with `pipeline::bam2mtx::anndata_output::AnnDataConfig { stranded: true, threads: 2, chunk_size: 4, batch_size: 4, triplet_spill_nnz: 8, ..Default::default() }` and removing relevant reassignments [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1430:9 [INFO] [stdout] | [INFO] [stdout] 1430 | let mut config = AnnDataConfig::default(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#field_reassign_with_default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: casting to the same type is unnecessary (`usize` -> `usize`) [INFO] [stdout] --> src/commands/bam2mtx/mod.rs:79:29 [INFO] [stdout] | [INFO] [stdout] 79 | triplet_spill_nnz: (chunk_size as usize * 16).max(500_000), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: try: `chunk_size` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field assignment outside of initializer for an instance created with Default::default() [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1511:9 [INFO] [stdout] | [INFO] [stdout] 1511 | config.stranded = true; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: consider initializing the variable with `pipeline::bam2mtx::anndata_output::AnnDataConfig { stranded: true, threads: 2, chunk_size: 4, batch_size: 4, triplet_spill_nnz: 4, ..Default::default() }` and removing relevant reassignments [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1510:9 [INFO] [stdout] | [INFO] [stdout] 1510 | let mut config = AnnDataConfig::default(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#field_reassign_with_default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field assignment outside of initializer for an instance created with Default::default() [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1615:9 [INFO] [stdout] | [INFO] [stdout] 1615 | config.stranded = false; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: consider initializing the variable with `pipeline::bam2mtx::anndata_output::AnnDataConfig { stranded: false, triplet_spill_nnz: 2, ..Default::default() }` and removing relevant reassignments [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1614:9 [INFO] [stdout] | [INFO] [stdout] 1614 | let mut config = AnnDataConfig::default(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#field_reassign_with_default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field assignment outside of initializer for an instance created with Default::default() [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1847:9 [INFO] [stdout] | [INFO] [stdout] 1847 | config.stranded = false; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: consider initializing the variable with `pipeline::bam2mtx::anndata_output::AnnDataConfig { stranded: false, triplet_spill_nnz: 100, ..Default::default() }` and removing relevant reassignments [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1846:9 [INFO] [stdout] | [INFO] [stdout] 1846 | let mut config = AnnDataConfig::default(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#field_reassign_with_default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field assignment outside of initializer for an instance created with Default::default() [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1878:9 [INFO] [stdout] | [INFO] [stdout] 1878 | config.stranded = false; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: consider initializing the variable with `pipeline::bam2mtx::anndata_output::AnnDataConfig { stranded: false, triplet_spill_nnz: 100, ..Default::default() }` and removing relevant reassignments [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1877:9 [INFO] [stdout] | [INFO] [stdout] 1877 | let mut config = AnnDataConfig::default(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#field_reassign_with_default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field assignment outside of initializer for an instance created with Default::default() [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1907:9 [INFO] [stdout] | [INFO] [stdout] 1907 | config.stranded = false; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: consider initializing the variable with `pipeline::bam2mtx::anndata_output::AnnDataConfig { stranded: false, triplet_spill_nnz: 100, ..Default::default() }` and removing relevant reassignments [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1906:9 [INFO] [stdout] | [INFO] [stdout] 1906 | let mut config = AnnDataConfig::default(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#field_reassign_with_default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: redundant closure [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1954:59 [INFO] [stdout] | [INFO] [stdout] 1954 | let identity_remap: Vec> = (0..2).map(|i| Some(i)).collect(); [INFO] [stdout] | ^^^^^^^^^^^ help: replace the closure with the tuple variant itself: `Some` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field assignment outside of initializer for an instance created with Default::default() [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:2018:9 [INFO] [stdout] | [INFO] [stdout] 2018 | config.stranded = false; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: consider initializing the variable with `pipeline::bam2mtx::anndata_output::AnnDataConfig { stranded: false, triplet_spill_nnz: 100, ..Default::default() }` and removing relevant reassignments [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:2017:9 [INFO] [stdout] | [INFO] [stdout] 2017 | let mut config = AnnDataConfig::default(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#field_reassign_with_default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: empty string literal in `writeln!` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/barcode.rs:153:9 [INFO] [stdout] | [INFO] [stdout] 153 | writeln!(file, "").unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^----^ [INFO] [stdout] | | [INFO] [stdout] | help: remove the empty string [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#writeln_empty_string [INFO] [stdout] = note: `#[warn(clippy::writeln_empty_string)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: casting to the same type is unnecessary (`u32` -> `u32`) [INFO] [stdout] --> src/lib/pipeline/bam2mtx/processor.rs:270:16 [INFO] [stdout] | [INFO] [stdout] 270 | if (pileup.depth() as u32) >= self.config.max_depth { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: try: `pileup.depth()` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast [INFO] [stdout] = note: `#[warn(clippy::unnecessary_cast)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: casting to the same type is unnecessary (`u32` -> `u32`) [INFO] [stdout] --> src/lib/pipeline/bam2mtx/processor.rs:425:16 [INFO] [stdout] | [INFO] [stdout] 425 | if (pileup.depth() as u32) >= config.max_depth { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: try: `pileup.depth()` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: redundant closure [INFO] [stdout] --> src/lib/pipeline/call/anndata_ops.rs:106:18 [INFO] [stdout] | [INFO] [stdout] 106 | .map(|m| SparseOps::estimate_csr_bytes(m)) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace the closure with the associated function itself: `SparseOps::estimate_csr_bytes` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: redundant closure [INFO] [stdout] --> src/lib/pipeline/call/anndata_ops.rs:123:30 [INFO] [stdout] | [INFO] [stdout] 123 | .map_err(|e| RedicatError::Io(e))?, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: replace the closure with the tuple variant itself: `RedicatError::Io` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_closure [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: using `contains()` instead of `iter().any()` is more efficient [INFO] [stdout] --> src/lib/pipeline/call/anndata_ops.rs:174:38 [INFO] [stdout] | [INFO] [stdout] 174 | .filter(|(name, _)| !keep.iter().any(|&k| k == name.as_str())) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `keep.contains(&name.as_str())` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_contains [INFO] [stdout] = note: `#[warn(clippy::manual_contains)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: very complex type used. Consider factoring parts into `type` definitions [INFO] [stdout] --> src/lib/pipeline/call/editing_analysis.rs:170:6 [INFO] [stdout] | [INFO] [stdout] 170 | ) -> ( [INFO] [stdout] | ______^ [INFO] [stdout] 171 | | HashMap>, [INFO] [stdout] 172 | | HashMap>, [INFO] [stdout] 173 | | HashMap>, [INFO] [stdout] 174 | | ) { [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#type_complexity [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this function has too many arguments (8/7) [INFO] [stdout] --> src/lib/pipeline/call/editing_analysis.rs:408:1 [INFO] [stdout] | [INFO] [stdout] 408 | / pub fn annotate_variants_pipeline( [INFO] [stdout] 409 | | adata: AnnDataContainer, [INFO] [stdout] 410 | | editing_sites: Arc>, [INFO] [stdout] 411 | | reference: Arc, [INFO] [stdout] ... | [INFO] [stdout] 416 | | min_coverage: u32, [INFO] [stdout] 417 | | ) -> Result { [INFO] [stdout] | |_____________________________^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#too_many_arguments [INFO] [stdout] = note: `#[warn(clippy::too_many_arguments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this function has too many arguments (12/7) [INFO] [stdout] --> src/lib/pipeline/call/editing_analysis.rs:768:1 [INFO] [stdout] | [INFO] [stdout] 768 | / fn classify_mismatch_fast( [INFO] [stdout] 769 | | site_idx: usize, [INFO] [stdout] 770 | | coverage_slice: &[u32], [INFO] [stdout] 771 | | ref_strings: &[String], [INFO] [stdout] ... | [INFO] [stdout] 780 | | min_coverage: u32, [INFO] [stdout] 781 | | ) -> MismatchClassification { [INFO] [stdout] | |___________________________^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#too_many_arguments [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: useless use of `vec!` [INFO] [stdout] --> src/lib/pipeline/bam2mtx/anndata_output.rs:1740:28 [INFO] [stdout] | [INFO] [stdout] 1740 | let mut triplets = vec![ [INFO] [stdout] | ____________________________^ [INFO] [stdout] 1741 | | Triplet { row: 2, col: 1, value: 10 }, [INFO] [stdout] 1742 | | Triplet { row: 1, col: 3, value: 20 }, [INFO] [stdout] 1743 | | Triplet { row: 1, col: 1, value: 30 }, [INFO] [stdout] 1744 | | Triplet { row: 0, col: 5, value: 40 }, [INFO] [stdout] 1745 | | Triplet { row: 2, col: 0, value: 50 }, [INFO] [stdout] 1746 | | ]; [INFO] [stdout] | |_________^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_vec [INFO] [stdout] = note: `#[warn(clippy::useless_vec)]` on by default [INFO] [stdout] help: you can use an array directly [INFO] [stdout] | [INFO] [stdout] 1740 ~ let mut triplets = [Triplet { row: 2, col: 1, value: 10 }, [INFO] [stdout] 1741 + Triplet { row: 1, col: 3, value: 20 }, [INFO] [stdout] 1742 + Triplet { row: 1, col: 1, value: 30 }, [INFO] [stdout] 1743 + Triplet { row: 0, col: 5, value: 40 }, [INFO] [stdout] 1744 ~ Triplet { row: 2, col: 0, value: 50 }]; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 7m 02s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1, rstest v0.11.0 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 4` [INFO] running `Command { std: "docker" "inspect" "b2b867a1605a85ac5724d044d9628870e46fbae4fa0a3502c165c2a3f3fde1d1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b2b867a1605a85ac5724d044d9628870e46fbae4fa0a3502c165c2a3f3fde1d1", kill_on_drop: false }` [INFO] [stdout] b2b867a1605a85ac5724d044d9628870e46fbae4fa0a3502c165c2a3f3fde1d1