[INFO] fetching crate modtector 0.15.4... [INFO] testing modtector-0.15.4 against master#d933cf483edf1605142ac6899ff32536c0ad8b22 for pr-150933 [INFO] extracting crate modtector 0.15.4 into /workspace/builds/worker-0-tc1/source [INFO] started tweaking crates.io crate modtector 0.15.4 [INFO] finished tweaking crates.io crate modtector 0.15.4 [INFO] tweaked toml for crates.io crate modtector 0.15.4 written to /workspace/builds/worker-0-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate modtector 0.15.4 on toolchain d933cf483edf1605142ac6899ff32536c0ad8b22 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+d933cf483edf1605142ac6899ff32536c0ad8b22" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate modtector 0.15.4 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" "+d933cf483edf1605142ac6899ff32536c0ad8b22" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded thiserror v1.0.63 [INFO] [stderr] Downloaded thiserror-impl v1.0.63 [INFO] [stderr] Downloaded quote v1.0.37 [INFO] [stderr] Downloaded wio v0.2.2 [INFO] [stderr] Downloaded derive-new v0.6.0 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded dirs-sys v0.5.0 [INFO] [stderr] Downloaded colorchoice v1.0.4 [INFO] [stderr] Downloaded yeslogic-fontconfig-sys v6.0.0 [INFO] [stderr] Downloaded derive-new v0.5.9 [INFO] [stderr] Downloaded once_cell_polyfill v1.70.1 [INFO] [stderr] Downloaded quick-error v1.2.3 [INFO] [stderr] Downloaded windows-implement v0.60.0 [INFO] [stderr] Downloaded strum v0.26.3 [INFO] [stderr] Downloaded dirs v6.0.0 [INFO] [stderr] Downloaded nalgebra-macros v0.2.2 [INFO] [stderr] Downloaded redox_users v0.5.0 [INFO] [stderr] Downloaded anstyle-query v1.1.3 [INFO] [stderr] Downloaded anstream v0.6.19 [INFO] [stderr] Downloaded core-text v20.1.0 [INFO] [stderr] Downloaded fixedbitset v0.4.2 [INFO] [stderr] Downloaded 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"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" "+d933cf483edf1605142ac6899ff32536c0ad8b22" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 6fd304f0f4f000073103e7ac3feaae468fb5e5dd2da5565531fa2a7ed3c9d68e [INFO] running `Command { std: "docker" "start" "-a" "6fd304f0f4f000073103e7ac3feaae468fb5e5dd2da5565531fa2a7ed3c9d68e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "6fd304f0f4f000073103e7ac3feaae468fb5e5dd2da5565531fa2a7ed3c9d68e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6fd304f0f4f000073103e7ac3feaae468fb5e5dd2da5565531fa2a7ed3c9d68e", kill_on_drop: false }` [INFO] [stdout] 6fd304f0f4f000073103e7ac3feaae468fb5e5dd2da5565531fa2a7ed3c9d68e [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+d933cf483edf1605142ac6899ff32536c0ad8b22" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 6372f9b8259f7a38c8d5fc9e29cda21e8f31d438248269c0cae7df157959d64c [INFO] running `Command { std: "docker" "start" "-a" "6372f9b8259f7a38c8d5fc9e29cda21e8f31d438248269c0cae7df157959d64c", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.158 [INFO] [stderr] Compiling pkg-config v0.3.30 [INFO] [stderr] Compiling libm v0.2.8 [INFO] [stderr] Compiling vcpkg v0.2.15 [INFO] [stderr] Compiling semver v1.0.26 [INFO] [stderr] Compiling glob v0.3.1 [INFO] [stderr] Compiling lazy_static v1.5.0 [INFO] [stderr] Compiling bytemuck v1.18.0 [INFO] [stderr] Compiling serde_core v1.0.228 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling libloading v0.8.5 [INFO] [stderr] Compiling simd-adler32 v0.3.7 [INFO] [stderr] Compiling regex-syntax v0.8.6 [INFO] [stderr] Compiling bitflags v2.6.0 [INFO] [stderr] Compiling serde v1.0.228 [INFO] [stderr] 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rust-htslib v0.47.0 [INFO] [stderr] Compiling modtector v0.15.4 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused imports: `AtomicUsize` and `Ordering` [INFO] [stdout] --> src/main.rs:14:25 [INFO] [stdout] | [INFO] [stdout] 14 | use std::sync::atomic::{AtomicUsize, Ordering}; [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 import: `std::sync::Arc` [INFO] [stdout] --> src/main.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 15 | use std::sync::Arc; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Array1` and `Array2` [INFO] [stdout] --> src/main.rs:22:15 [INFO] [stdout] | [INFO] [stdout] 22 | use ndarray::{Array1, Array2}; [INFO] [stdout] | ^^^^^^ ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/convert.rs:1313:9 [INFO] [stdout] | [INFO] [stdout] 1313 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/correct.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around function argument [INFO] [stdout] --> src/duet.rs:2823:21 [INFO] [stdout] | [INFO] [stdout] 2823 | ((165.0 * (1.0 - t)) as u8), [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] 2823 - ((165.0 * (1.0 - t)) as u8), [INFO] [stdout] 2823 + (165.0 * (1.0 - t)) as u8 , [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around function argument [INFO] [stdout] --> src/duet.rs:2866:17 [INFO] [stdout] | [INFO] [stdout] 2866 | ((165.0 * (1.0 - t)) as u8), [INFO] [stdout] | ^ ^ [INFO] [stdout] | [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 2866 - ((165.0 * (1.0 - t)) as u8), [INFO] [stdout] 2866 + (165.0 * (1.0 - t)) as u8 , [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Read` [INFO] [stdout] --> src/reactivity.rs:7:42 [INFO] [stdout] | [INFO] [stdout] 7 | use std::io::{BufRead, BufReader, Write, Read}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `n` [INFO] [stdout] --> src/compare.rs:325:9 [INFO] [stdout] | [INFO] [stdout] 325 | let n = base.len(); [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_n` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/compare.rs:391:13 [INFO] [stdout] | [INFO] [stdout] 391 | let mut region_start = i; [INFO] [stdout] | ----^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `window_radius` [INFO] [stdout] --> src/compare.rs:355:5 [INFO] [stdout] | [INFO] [stdout] 355 | window_radius: usize, [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_window_radius` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/convert.rs:867:28 [INFO] [stdout] | [INFO] [stdout] 867 | let (mut ref_base, mut mutation_count, mut rt_stops, mut coverage) = [INFO] [stdout] | ----^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `args` [INFO] [stdout] --> src/convert.rs:1052:5 [INFO] [stdout] | [INFO] [stdout] 1052 | args: &ConvertArgs, [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_args` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `in_transcript` is assigned to, but never used [INFO] [stdout] --> src/convert.rs:1204:9 [INFO] [stdout] | [INFO] [stdout] 1204 | let mut in_transcript = false; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_in_transcript` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `in_transcript` is never read [INFO] [stdout] --> src/convert.rs:1214:25 [INFO] [stdout] | [INFO] [stdout] 1214 | in_transcript = true; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `in_transcript` is never read [INFO] [stdout] --> src/convert.rs:1246:25 [INFO] [stdout] | [INFO] [stdout] 1246 | in_transcript = false; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/convert.rs:1858:9 [INFO] [stdout] | [INFO] [stdout] 1858 | let mut line_iter = reader.lines(); [INFO] [stdout] | ----^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `key` [INFO] [stdout] --> src/convert.rs:2095:10 [INFO] [stdout] | [INFO] [stdout] 2095 | for (key, mut entries) in entries_by_key { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_key` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `df` [INFO] [stdout] --> src/correct.rs:32:9 [INFO] [stdout] | [INFO] [stdout] 32 | let df = 2.0; [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_df` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `p` is never read [INFO] [stdout] --> src/correct.rs:122:26 [INFO] [stdout] | [INFO] [stdout] 122 | let mut p: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `q` is never read [INFO] [stdout] --> src/correct.rs:123:26 [INFO] [stdout] | [INFO] [stdout] 123 | let mut q: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `r` is never read [INFO] [stdout] --> src/correct.rs:124:26 [INFO] [stdout] | [INFO] [stdout] 124 | let mut r: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `max_mutation` [INFO] [stdout] --> src/correct.rs:344:9 [INFO] [stdout] | [INFO] [stdout] 344 | let max_mutation = binned.iter().map(|(_, mr)| *mr).fold(0.0, f64::max); [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_mutation` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mutation_rate` [INFO] [stdout] --> src/correct.rs:394:5 [INFO] [stdout] | [INFO] [stdout] 394 | mutation_rate: f64, [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mutation_rate` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `weight_decrease` [INFO] [stdout] --> src/correct.rs:398:5 [INFO] [stdout] | [INFO] [stdout] 398 | weight_decrease: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_weight_decrease` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/duet.rs:2697:9 [INFO] [stdout] | [INFO] [stdout] 2697 | let mut reordered_ensemble_ids: Vec = row_order.iter().map(|&idx| ensemble_ids[idx]).collect(); [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/duet.rs:2698:9 [INFO] [stdout] | [INFO] [stdout] 2698 | let mut reordered_matrix: Vec> = row_order.iter().map(|&idx| reactivity_matrix[idx].clone()).collect(); [INFO] [stdout] | ----^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `base_plot_height` [INFO] [stdout] --> src/duet.rs:2724:9 [INFO] [stdout] | [INFO] [stdout] 2724 | let base_plot_height = 800; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_base_plot_height` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ensemble` [INFO] [stdout] --> src/duet.rs:3033:21 [INFO] [stdout] | [INFO] [stdout] 3033 | if let Some(ensemble) = global_ensembles.iter().find(|e| e.id == ensemble_id) { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ensemble` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `range` [INFO] [stdout] --> src/duet.rs:3244:21 [INFO] [stdout] | [INFO] [stdout] 3244 | let range = max_pos - min_pos; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_range` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `idx` [INFO] [stdout] --> src/duet.rs:3417:10 [INFO] [stdout] | [INFO] [stdout] 3417 | for (idx, (pos, reactivity)) in full_reactivity_data.iter().enumerate() { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_idx` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `idx` [INFO] [stdout] --> src/duet.rs:3445:10 [INFO] [stdout] | [INFO] [stdout] 3445 | for (idx, (pos, reactivity)) in non_full_reactivity_data.iter().enumerate() { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_idx` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/duet.rs:3743:9 [INFO] [stdout] | [INFO] [stdout] 3743 | let mut sigmas: Vec = knn_distances.iter().map(|dists| { [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `p` [INFO] [stdout] --> src/duet.rs:3708:9 [INFO] [stdout] | [INFO] [stdout] 3708 | let p = data[0].len(); [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_p` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/duet.rs:3830:9 [INFO] [stdout] | [INFO] [stdout] 3830 | let mut cluster_distances: Vec> = distances.clone(); [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `cluster_distances` [INFO] [stdout] --> src/duet.rs:3830:9 [INFO] [stdout] | [INFO] [stdout] 3830 | let mut cluster_distances: Vec> = distances.clone(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_cluster_distances` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/duet.rs:3890:9 [INFO] [stdout] | [INFO] [stdout] 3890 | let mut centered: Vec> = data.iter().map(|row| { [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `single_stranded_count` [INFO] [stdout] --> src/evaluate.rs:136:9 [INFO] [stdout] | [INFO] [stdout] 136 | let single_stranded_count = is_single_stranded.iter().filter(|&&x| x).count(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_single_stranded_count` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `double_stranded_count` [INFO] [stdout] --> src/evaluate.rs:137:9 [INFO] [stdout] | [INFO] [stdout] 137 | let double_stranded_count = is_single_stranded.iter().filter(|&&x| !x).count(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_double_stranded_count` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `total_lines` [INFO] [stdout] --> src/evaluate.rs:159:9 [INFO] [stdout] | [INFO] [stdout] 159 | let total_lines = std::fs::read_to_string(csv_file)?.lines().count(); [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_total_lines` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `match_rate` [INFO] [stdout] --> src/evaluate.rs:336:9 [INFO] [stdout] | [INFO] [stdout] 336 | let match_rate = if best_match_count > 0 { [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_match_rate` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `match_count` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:344:9 [INFO] [stdout] | [INFO] [stdout] 344 | let mut match_count = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_match_count` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `mismatch_count` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:345:9 [INFO] [stdout] | [INFO] [stdout] 345 | let mut mismatch_count = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_mismatch_count` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `skipped_count` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:346:9 [INFO] [stdout] | [INFO] [stdout] 346 | let mut skipped_count = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_skipped_count` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `match_count` is never read [INFO] [stdout] --> src/evaluate.rs:360:21 [INFO] [stdout] | [INFO] [stdout] 360 | match_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `mismatch_count` is never read [INFO] [stdout] --> src/evaluate.rs:362:21 [INFO] [stdout] | [INFO] [stdout] 362 | mismatch_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `skipped_count` is never read [INFO] [stdout] --> src/evaluate.rs:370:13 [INFO] [stdout] | [INFO] [stdout] 370 | skipped_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `skipped_count` is never read [INFO] [stdout] --> src/evaluate.rs:366:17 [INFO] [stdout] | [INFO] [stdout] 366 | skipped_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `thresholds` is never read [INFO] [stdout] --> src/evaluate.rs:624:26 [INFO] [stdout] | [INFO] [stdout] 624 | let mut thresholds = Vec::new(); [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `tn` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:1579:13 [INFO] [stdout] | [INFO] [stdout] 1579 | let mut tn = 0; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_tn` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `fn_count` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:1580:13 [INFO] [stdout] | [INFO] [stdout] 1580 | let mut fn_count = 0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_fn_count` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `tn` is never read [INFO] [stdout] --> src/evaluate.rs:1597:21 [INFO] [stdout] | [INFO] [stdout] 1597 | tn += 1; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `fn_count` is never read [INFO] [stdout] --> src/evaluate.rs:1595:21 [INFO] [stdout] | [INFO] [stdout] 1595 | fn_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `data` [INFO] [stdout] --> src/evaluate.rs:1839:16 [INFO] [stdout] | [INFO] [stdout] 1839 | for (base, data) in &base_groups { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_data` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `auc` [INFO] [stdout] --> src/evaluate.rs:1900:37 [INFO] [stdout] | [INFO] [stdout] 1900 | ... let auc = result.auc; [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_auc` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `signal_type` [INFO] [stdout] --> src/evaluate.rs:1952:5 [INFO] [stdout] | [INFO] [stdout] 1952 | signal_type: &str, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_signal_type` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `tn` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:2013:13 [INFO] [stdout] | [INFO] [stdout] 2013 | let mut tn = 0; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_tn` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `fn_count` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:2014:13 [INFO] [stdout] | [INFO] [stdout] 2014 | let mut fn_count = 0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_fn_count` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `tn` is never read [INFO] [stdout] --> src/evaluate.rs:2031:21 [INFO] [stdout] | [INFO] [stdout] 2031 | tn += 1; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `fn_count` is never read [INFO] [stdout] --> src/evaluate.rs:2029:21 [INFO] [stdout] | [INFO] [stdout] 2029 | fn_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_val` [INFO] [stdout] --> src/norm.rs:191:9 [INFO] [stdout] | [INFO] [stdout] 191 | let min_val = valid_values [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_val` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `logger` [INFO] [stdout] --> src/norm.rs:234:34 [INFO] [stdout] | [INFO] [stdout] 234 | pub fn norm_csv(args: &NormArgs, logger: &mut crate::Logger) -> Result<(), Box> { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_logger` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/norm.rs:510:9 [INFO] [stdout] | [INFO] [stdout] 510 | let mut window_start = 0; [INFO] [stdout] | ----^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `window_start` [INFO] [stdout] --> src/norm.rs:510:9 [INFO] [stdout] | [INFO] [stdout] 510 | let mut window_start = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_window_start` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `base_regex` [INFO] [stdout] --> src/plot.rs:99:9 [INFO] [stdout] | [INFO] [stdout] 99 | let base_regex = Regex::new(r"]*>([ATCGU])")?; [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_base_regex` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `skipped_lines` is assigned to, but never used [INFO] [stdout] --> src/plot.rs:283:9 [INFO] [stdout] | [INFO] [stdout] 283 | let mut skipped_lines = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_skipped_lines` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `total_lines` is assigned to, but never used [INFO] [stdout] --> src/plot.rs:284:9 [INFO] [stdout] | [INFO] [stdout] 284 | let mut total_lines = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_total_lines` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `skipped_lines` is never read [INFO] [stdout] --> src/plot.rs:295:13 [INFO] [stdout] | [INFO] [stdout] 295 | skipped_lines += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `total_lines` is never read [INFO] [stdout] --> src/plot.rs:290:9 [INFO] [stdout] | [INFO] [stdout] 290 | total_lines += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `written_lines` is assigned to, but never used [INFO] [stdout] --> src/plot.rs:316:9 [INFO] [stdout] | [INFO] [stdout] 316 | let mut written_lines = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_written_lines` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `written_lines` is never read [INFO] [stdout] --> src/plot.rs:330:13 [INFO] [stdout] | [INFO] [stdout] 330 | written_lines += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_pos2base` [INFO] [stdout] --> src/plot.rs:493:13 [INFO] [stdout] | [INFO] [stdout] 493 | let ref_pos2base = load_reference_sequence(ref_file)?; [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_pos2base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `is_stop_file` [INFO] [stdout] --> src/plot.rs:741:9 [INFO] [stdout] | [INFO] [stdout] 741 | let is_stop_file = csv_file.contains("stop"); [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_is_stop_file` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `is_mutation_file` [INFO] [stdout] --> src/plot.rs:742:9 [INFO] [stdout] | [INFO] [stdout] 742 | let is_mutation_file = csv_file.contains("mutation"); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_is_mutation_file` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reactivity_file` [INFO] [stdout] --> src/plot.rs:9018:5 [INFO] [stdout] | [INFO] [stdout] 9018 | reactivity_file: &str, [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reactivity_file` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `bases_filter` [INFO] [stdout] --> src/plot.rs:9021:5 [INFO] [stdout] | [INFO] [stdout] 9021 | bases_filter: &str, [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bases_filter` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `strand_filter` [INFO] [stdout] --> src/plot.rs:9023:5 [INFO] [stdout] | [INFO] [stdout] 9023 | strand_filter: &str, [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand_filter` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `id_regex` [INFO] [stdout] --> src/plot.rs:9101:9 [INFO] [stdout] | [INFO] [stdout] 9101 | let id_regex = Regex::new(r#"id="node_(\d+)""#)?; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_id_regex` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/progress.rs:85:29 [INFO] [stdout] | [INFO] [stdout] 85 | pub fn with_description(mut self, description: &str) -> io::Result<()> { [INFO] [stdout] | ----^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `best_threshold` is assigned to, but never used [INFO] [stdout] --> src/reactivity.rs:627:9 [INFO] [stdout] | [INFO] [stdout] 627 | let mut best_threshold = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_best_threshold` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_threshold` is never read [INFO] [stdout] --> src/reactivity.rs:666:13 [INFO] [stdout] | [INFO] [stdout] 666 | best_threshold = threshold; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `best_score_on_left` [INFO] [stdout] --> src/reactivity.rs:857:9 [INFO] [stdout] | [INFO] [stdout] 857 | let best_score_on_left = best_initial_k < 1.0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_best_score_on_left` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `best_coarse_auc` is assigned to, but never used [INFO] [stdout] --> src/reactivity.rs:893:9 [INFO] [stdout] | [INFO] [stdout] 893 | let mut best_coarse_auc = best_initial_auc; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_best_coarse_auc` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_score` is never read [INFO] [stdout] --> src/reactivity.rs:1002:13 [INFO] [stdout] | [INFO] [stdout] 1002 | best_coarse_score = score_left; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_score` is never read [INFO] [stdout] --> src/reactivity.rs:998:13 [INFO] [stdout] | [INFO] [stdout] 998 | best_coarse_score = score_right; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_score` is never read [INFO] [stdout] --> src/reactivity.rs:987:13 [INFO] [stdout] | [INFO] [stdout] 987 | best_coarse_score = score; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_score` is never read [INFO] [stdout] --> src/reactivity.rs:979:13 [INFO] [stdout] | [INFO] [stdout] 979 | best_coarse_score = score; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_auc` is never read [INFO] [stdout] --> src/reactivity.rs:1003:13 [INFO] [stdout] | [INFO] [stdout] 1003 | best_coarse_auc = auc_left; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_auc` is never read [INFO] [stdout] --> src/reactivity.rs:999:13 [INFO] [stdout] | [INFO] [stdout] 999 | best_coarse_auc = auc_right; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_auc` is never read [INFO] [stdout] --> src/reactivity.rs:988:13 [INFO] [stdout] | [INFO] [stdout] 988 | best_coarse_auc = auc; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_auc` is never read [INFO] [stdout] --> src/reactivity.rs:980:13 [INFO] [stdout] | [INFO] [stdout] 980 | best_coarse_auc = auc; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `df` [INFO] [stdout] --> src/main.rs:417:9 [INFO] [stdout] | [INFO] [stdout] 417 | let df = 2.0; [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_df` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `p` is never read [INFO] [stdout] --> src/main.rs:510:26 [INFO] [stdout] | [INFO] [stdout] 510 | let mut p: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `q` is never read [INFO] [stdout] --> src/main.rs:511:26 [INFO] [stdout] | [INFO] [stdout] 511 | let mut q: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `r` is never read [INFO] [stdout] --> src/main.rs:512:26 [INFO] [stdout] | [INFO] [stdout] 512 | let mut r: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `initial_params` [INFO] [stdout] --> src/main.rs:762:9 [INFO] [stdout] | [INFO] [stdout] 762 | let initial_params = vec![ [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_initial_params` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mutation_rate` [INFO] [stdout] --> src/main.rs:1202:5 [INFO] [stdout] | [INFO] [stdout] 1202 | mutation_rate: f64, [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mutation_rate` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `weight_decrease` [INFO] [stdout] --> src/main.rs:1206:5 [INFO] [stdout] | [INFO] [stdout] 1206 | weight_decrease: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_weight_decrease` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:1466:9 [INFO] [stdout] | [INFO] [stdout] 1466 | let mut expected_refs: HashSet = region_intervals.keys().cloned().collect(); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `num_threads` [INFO] [stdout] --> src/main.rs:1436:5 [INFO] [stdout] | [INFO] [stdout] 1436 | num_threads: usize, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_num_threads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `base_recommendation` [INFO] [stdout] --> src/main.rs:2950:9 [INFO] [stdout] | [INFO] [stdout] 2950 | let base_recommendation = (bam_file_count * 2).min(64); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_base_recommendation` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `completed` [INFO] [stdout] --> src/main.rs:3095:9 [INFO] [stdout] | [INFO] [stdout] 3095 | let completed = Arc::new(AtomicUsize::new(0)); [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_completed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_seq` [INFO] [stdout] --> src/main.rs:3359:24 [INFO] [stdout] | [INFO] [stdout] 3359 | for (ref_name, ref_seq) in &reference_sequences { [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_seq` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_name` [INFO] [stdout] --> src/main.rs:3727:10 [INFO] [stdout] | [INFO] [stdout] 3727 | for (ref_name, intervals) in &distribution { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_name` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_base` [INFO] [stdout] --> src/main.rs:3996:21 [INFO] [stdout] | [INFO] [stdout] 3996 | let ref_base = if pos < ref_seq.len() as u32 { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/main.rs:4444:9 [INFO] [stdout] | [INFO] [stdout] 4444 | let header = bam.header().to_owned(); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `PositionData` is more private than the item `ReplicateData::replicates` [INFO] [stdout] --> src/compare.rs:54:5 [INFO] [stdout] | [INFO] [stdout] 54 | pub replicates: Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ field `ReplicateData::replicates` is reachable at visibility `pub(crate)` [INFO] [stdout] | [INFO] [stdout] note: but type `PositionData` is only usable at visibility `pub(self)` [INFO] [stdout] --> src/compare.rs:110:1 [INFO] [stdout] | [INFO] [stdout] 110 | struct PositionData { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = note: `#[warn(private_interfaces)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `tid` is never read [INFO] [stdout] --> src/main.rs:398:5 [INFO] [stdout] | [INFO] [stdout] 397 | struct Item { [INFO] [stdout] | ---- field in this struct [INFO] [stdout] 398 | tid: String, [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Item` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `normalize_signal` is never used [INFO] [stdout] --> src/main.rs:1608:4 [INFO] [stdout] | [INFO] [stdout] 1608 | fn normalize_signal( [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: enum `CompareMode` is never used [INFO] [stdout] --> src/compare.rs:12:10 [INFO] [stdout] | [INFO] [stdout] 12 | pub enum CompareMode { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `test_type` is never read [INFO] [stdout] --> src/compare.rs:43:9 [INFO] [stdout] | [INFO] [stdout] 42 | pub struct StatisticalResult { [INFO] [stdout] | ----------------- field in this struct [INFO] [stdout] 43 | pub test_type: StatisticalTest, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `StatisticalResult` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `ReplicateData` is never constructed [INFO] [stdout] --> src/compare.rs:52:12 [INFO] [stdout] | [INFO] [stdout] 52 | pub struct ReplicateData { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `ComparisonResult` is never constructed [INFO] [stdout] --> src/compare.rs:59:12 [INFO] [stdout] | [INFO] [stdout] 59 | pub struct ComparisonResult { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `DiffScanResult` is never constructed [INFO] [stdout] --> src/compare.rs:73:12 [INFO] [stdout] | [INFO] [stdout] 73 | pub struct DiffScanResult { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `DeltaSHAPEResult` is never constructed [INFO] [stdout] --> src/compare.rs:89:12 [INFO] [stdout] | [INFO] [stdout] 89 | pub struct DeltaSHAPEResult { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `NormalizationParams` is never constructed [INFO] [stdout] --> src/compare.rs:104:12 [INFO] [stdout] | [INFO] [stdout] 104 | pub struct NormalizationParams { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `ins`, `del`, `a`, `c`, `g`, and `t` are never read [INFO] [stdout] --> src/compare.rs:118:5 [INFO] [stdout] | [INFO] [stdout] 110 | struct PositionData { [INFO] [stdout] | ------------ fields in this struct [INFO] [stdout] ... [INFO] [stdout] 118 | ins: usize, [INFO] [stdout] | ^^^ [INFO] [stdout] 119 | del: usize, [INFO] [stdout] | ^^^ [INFO] [stdout] 120 | a: u32, [INFO] [stdout] | ^ [INFO] [stdout] 121 | c: u32, [INFO] [stdout] | ^ [INFO] [stdout] 122 | g: u32, [INFO] [stdout] | ^ [INFO] [stdout] 123 | t: u32, [INFO] [stdout] | ^ [INFO] [stdout] | [INFO] [stdout] = note: `PositionData` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `normalize_reactivity_data` is never used [INFO] [stdout] --> src/compare.rs:437:4 [INFO] [stdout] | [INFO] [stdout] 437 | fn normalize_reactivity_data( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `quantile_normalization` is never used [INFO] [stdout] --> src/compare.rs:451:4 [INFO] [stdout] | [INFO] [stdout] 451 | fn quantile_normalization( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `robust_normalization` is never used [INFO] [stdout] --> src/compare.rs:500:4 [INFO] [stdout] | [INFO] [stdout] 500 | fn robust_normalization( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `median_normalization` is never used [INFO] [stdout] --> src/compare.rs:535:4 [INFO] [stdout] | [INFO] [stdout] 535 | fn median_normalization( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_mad` is never used [INFO] [stdout] --> src/compare.rs:575:4 [INFO] [stdout] | [INFO] [stdout] 575 | fn calculate_mad(values: &[f64], median: f64) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compare_samples` is never used [INFO] [stdout] --> src/compare.rs:1764:8 [INFO] [stdout] | [INFO] [stdout] 1764 | pub fn compare_samples( [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_reference_sequence` is never used [INFO] [stdout] --> src/convert.rs:372:4 [INFO] [stdout] | [INFO] [stdout] 372 | fn load_reference_sequence(fasta_path: &str, chr_name: Option<&str>) -> Result, Box> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `MIN_SHARED_FRACTION` is never used [INFO] [stdout] --> src/duet.rs:29:7 [INFO] [stdout] | [INFO] [stdout] 29 | const MIN_SHARED_FRACTION: f64 = 0.15; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `MIN_REACTIVITY_CORRELATION` is never used [INFO] [stdout] --> src/duet.rs:33:7 [INFO] [stdout] | [INFO] [stdout] 33 | const MIN_REACTIVITY_CORRELATION: f64 = 0.60; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `plot_single_track` is never used [INFO] [stdout] --> src/duet.rs:3555:4 [INFO] [stdout] | [INFO] [stdout] 3555 | fn plot_single_track( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `ReactivityData` is never constructed [INFO] [stdout] --> src/norm.rs:97:8 [INFO] [stdout] | [INFO] [stdout] 97 | struct ReactivityData { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `dynamic_window_norm` is never used [INFO] [stdout] --> src/norm.rs:475:4 [INFO] [stdout] | [INFO] [stdout] 475 | fn dynamic_window_norm( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_adaptive_window` is never used [INFO] [stdout] --> src/norm.rs:581:4 [INFO] [stdout] | [INFO] [stdout] 581 | fn find_adaptive_window( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_dynamic_window` is never used [INFO] [stdout] --> src/norm.rs:620:4 [INFO] [stdout] | [INFO] [stdout] 620 | fn find_dynamic_window( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `normalize_window` is never used [INFO] [stdout] --> src/norm.rs:630:4 [INFO] [stdout] | [INFO] [stdout] 630 | fn normalize_window(values: &[f64], norm_method: &StopNormMethod) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `SvgElement` is never constructed [INFO] [stdout] --> src/plot.rs:75:12 [INFO] [stdout] | [INFO] [stdout] 75 | pub struct SvgElement { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `is_high` is never read [INFO] [stdout] --> src/plot.rs:663:5 [INFO] [stdout] | [INFO] [stdout] 657 | struct GenePlotTask { [INFO] [stdout] | ------------ field in this struct [INFO] [stdout] ... [INFO] [stdout] 663 | is_high: bool, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `GenePlotTask` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `gene_id` and `cov_x_depth` are never read [INFO] [stdout] --> src/plot.rs:668:5 [INFO] [stdout] | [INFO] [stdout] 667 | struct GeneStat { [INFO] [stdout] | -------- fields in this struct [INFO] [stdout] 668 | gene_id: String, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 671 | cov_x_depth: f64, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `GeneStat` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_best_shift_for_base` is never used [INFO] [stdout] --> src/plot.rs:2155:8 [INFO] [stdout] | [INFO] [stdout] 2155 | pub fn find_best_shift_for_base( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `ProgressBar` is never constructed [INFO] [stdout] --> src/progress.rs:4:12 [INFO] [stdout] | [INFO] [stdout] 4 | pub struct ProgressBar { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `with_width`, `update`, `display`, `finish`, and `with_description` are never used [INFO] [stdout] --> src/progress.rs:13:12 [INFO] [stdout] | [INFO] [stdout] 11 | impl ProgressBar { [INFO] [stdout] | ---------------- associated items in this implementation [INFO] [stdout] 12 | /// Create a new progress bar [INFO] [stdout] 13 | pub fn new(total: usize) -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 23 | pub fn with_width(mut self, width: usize) -> Self { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 29 | pub fn update(&mut self, current: usize) -> io::Result<()> { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 47 | fn display(&self) -> io::Result<()> { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 77 | pub fn finish(&mut self) -> io::Result<()> { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 85 | pub fn with_description(mut self, description: &str) -> io::Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `DescriptiveProgress` is never constructed [INFO] [stdout] --> src/progress.rs:162:12 [INFO] [stdout] | [INFO] [stdout] 162 | pub struct DescriptiveProgress { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `update`, and `finish` are never used [INFO] [stdout] --> src/progress.rs:171:12 [INFO] [stdout] | [INFO] [stdout] 169 | impl DescriptiveProgress { [INFO] [stdout] | ------------------------ associated items in this implementation [INFO] [stdout] 170 | /// Create a new descriptive progress displayer [INFO] [stdout] 171 | pub fn new(total: usize, description: &str) -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 181 | pub fn update(&mut self, current: usize) -> io::Result<()> { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 203 | pub fn finish(&mut self) -> io::Result<()> { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `vs_low_p50`, `vs_overall_p50`, and `correction_p50` are never read [INFO] [stdout] --> src/reactivity.rs:270:5 [INFO] [stdout] | [INFO] [stdout] 267 | struct DistributionTargets { [INFO] [stdout] | ------------------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 270 | vs_low_p50: f64, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 277 | vs_overall_p50: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 284 | correction_p50: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_auc_for_k` is never used [INFO] [stdout] --> src/reactivity.rs:713:4 [INFO] [stdout] | [INFO] [stdout] 713 | fn calculate_auc_for_k( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:1442:5 [INFO] [stdout] | [INFO] [stdout] 1442 | bam.set_threads(1); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] = note: `#[warn(unused_must_use)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 1442 | let _ = bam.set_threads(1); [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:3493:13 [INFO] [stdout] | [INFO] [stdout] 3493 | bam.set_threads(1); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 3493 | let _ = bam.set_threads(1); [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:4442:5 [INFO] [stdout] | [INFO] [stdout] 4442 | bam.set_threads(1); // Avoid internal multi-threading conflicts [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 4442 | let _ = bam.set_threads(1); // Avoid internal multi-threading conflicts [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:4475:9 [INFO] [stdout] | [INFO] [stdout] 4475 | window_bam.set_threads(1); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 4475 | let _ = window_bam.set_threads(1); [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: comparison is useless due to type limits [INFO] [stdout] --> src/main.rs:4549:32 [INFO] [stdout] | [INFO] [stdout] 4549 | ... if qpos >= 0 && (qpos as usize) < quals.len() { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_comparisons)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compute_scan_Q` should have a snake case name [INFO] [stdout] --> src/compare.rs:274:4 [INFO] [stdout] | [INFO] [stdout] 274 | fn compute_scan_Q( [INFO] [stdout] | ^^^^^^^^^^^^^^ help: convert the identifier to snake case: `compute_scan_q` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 06s [INFO] running `Command { std: "docker" "inspect" "6372f9b8259f7a38c8d5fc9e29cda21e8f31d438248269c0cae7df157959d64c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6372f9b8259f7a38c8d5fc9e29cda21e8f31d438248269c0cae7df157959d64c", kill_on_drop: false }` [INFO] [stdout] 6372f9b8259f7a38c8d5fc9e29cda21e8f31d438248269c0cae7df157959d64c [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+d933cf483edf1605142ac6899ff32536c0ad8b22" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 78eb208184dae26e70eb02a5ac11d1aa2c32d95b51d4f7b8293eaeb96dae4cfc [INFO] running `Command { std: "docker" "start" "-a" "78eb208184dae26e70eb02a5ac11d1aa2c32d95b51d4f7b8293eaeb96dae4cfc", kill_on_drop: false }` [INFO] [stderr] Compiling modtector v0.15.4 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused imports: `AtomicUsize` and `Ordering` [INFO] [stdout] --> src/main.rs:14:25 [INFO] [stdout] | [INFO] [stdout] 14 | use std::sync::atomic::{AtomicUsize, Ordering}; [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 import: `std::sync::Arc` [INFO] [stdout] --> src/main.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 15 | use std::sync::Arc; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Array1` and `Array2` [INFO] [stdout] --> src/main.rs:22:15 [INFO] [stdout] | [INFO] [stdout] 22 | use ndarray::{Array1, Array2}; [INFO] [stdout] | ^^^^^^ ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/convert.rs:1313:9 [INFO] [stdout] | [INFO] [stdout] 1313 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/correct.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around function argument [INFO] [stdout] --> src/duet.rs:2823:21 [INFO] [stdout] | [INFO] [stdout] 2823 | ((165.0 * (1.0 - t)) as u8), [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] 2823 - ((165.0 * (1.0 - t)) as u8), [INFO] [stdout] 2823 + (165.0 * (1.0 - t)) as u8 , [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around function argument [INFO] [stdout] --> src/duet.rs:2866:17 [INFO] [stdout] | [INFO] [stdout] 2866 | ((165.0 * (1.0 - t)) as u8), [INFO] [stdout] | ^ ^ [INFO] [stdout] | [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 2866 - ((165.0 * (1.0 - t)) as u8), [INFO] [stdout] 2866 + (165.0 * (1.0 - t)) as u8 , [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Read` [INFO] [stdout] --> src/reactivity.rs:7:42 [INFO] [stdout] | [INFO] [stdout] 7 | use std::io::{BufRead, BufReader, Write, Read}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `n` [INFO] [stdout] --> src/compare.rs:325:9 [INFO] [stdout] | [INFO] [stdout] 325 | let n = base.len(); [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_n` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/compare.rs:391:13 [INFO] [stdout] | [INFO] [stdout] 391 | let mut region_start = i; [INFO] [stdout] | ----^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `window_radius` [INFO] [stdout] --> src/compare.rs:355:5 [INFO] [stdout] | [INFO] [stdout] 355 | window_radius: usize, [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_window_radius` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/convert.rs:867:28 [INFO] [stdout] | [INFO] [stdout] 867 | let (mut ref_base, mut mutation_count, mut rt_stops, mut coverage) = [INFO] [stdout] | ----^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `args` [INFO] [stdout] --> src/convert.rs:1052:5 [INFO] [stdout] | [INFO] [stdout] 1052 | args: &ConvertArgs, [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_args` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `in_transcript` is assigned to, but never used [INFO] [stdout] --> src/convert.rs:1204:9 [INFO] [stdout] | [INFO] [stdout] 1204 | let mut in_transcript = false; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_in_transcript` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `in_transcript` is never read [INFO] [stdout] --> src/convert.rs:1214:25 [INFO] [stdout] | [INFO] [stdout] 1214 | in_transcript = true; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `in_transcript` is never read [INFO] [stdout] --> src/convert.rs:1246:25 [INFO] [stdout] | [INFO] [stdout] 1246 | in_transcript = false; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/convert.rs:1858:9 [INFO] [stdout] | [INFO] [stdout] 1858 | let mut line_iter = reader.lines(); [INFO] [stdout] | ----^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `key` [INFO] [stdout] --> src/convert.rs:2095:10 [INFO] [stdout] | [INFO] [stdout] 2095 | for (key, mut entries) in entries_by_key { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_key` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `df` [INFO] [stdout] --> src/correct.rs:32:9 [INFO] [stdout] | [INFO] [stdout] 32 | let df = 2.0; [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_df` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `p` is never read [INFO] [stdout] --> src/correct.rs:122:26 [INFO] [stdout] | [INFO] [stdout] 122 | let mut p: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `q` is never read [INFO] [stdout] --> src/correct.rs:123:26 [INFO] [stdout] | [INFO] [stdout] 123 | let mut q: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `r` is never read [INFO] [stdout] --> src/correct.rs:124:26 [INFO] [stdout] | [INFO] [stdout] 124 | let mut r: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `max_mutation` [INFO] [stdout] --> src/correct.rs:344:9 [INFO] [stdout] | [INFO] [stdout] 344 | let max_mutation = binned.iter().map(|(_, mr)| *mr).fold(0.0, f64::max); [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_mutation` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mutation_rate` [INFO] [stdout] --> src/correct.rs:394:5 [INFO] [stdout] | [INFO] [stdout] 394 | mutation_rate: f64, [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mutation_rate` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `weight_decrease` [INFO] [stdout] --> src/correct.rs:398:5 [INFO] [stdout] | [INFO] [stdout] 398 | weight_decrease: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_weight_decrease` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/duet.rs:2697:9 [INFO] [stdout] | [INFO] [stdout] 2697 | let mut reordered_ensemble_ids: Vec = row_order.iter().map(|&idx| ensemble_ids[idx]).collect(); [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/duet.rs:2698:9 [INFO] [stdout] | [INFO] [stdout] 2698 | let mut reordered_matrix: Vec> = row_order.iter().map(|&idx| reactivity_matrix[idx].clone()).collect(); [INFO] [stdout] | ----^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `base_plot_height` [INFO] [stdout] --> src/duet.rs:2724:9 [INFO] [stdout] | [INFO] [stdout] 2724 | let base_plot_height = 800; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_base_plot_height` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ensemble` [INFO] [stdout] --> src/duet.rs:3033:21 [INFO] [stdout] | [INFO] [stdout] 3033 | if let Some(ensemble) = global_ensembles.iter().find(|e| e.id == ensemble_id) { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ensemble` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `range` [INFO] [stdout] --> src/duet.rs:3244:21 [INFO] [stdout] | [INFO] [stdout] 3244 | let range = max_pos - min_pos; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_range` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `idx` [INFO] [stdout] --> src/duet.rs:3417:10 [INFO] [stdout] | [INFO] [stdout] 3417 | for (idx, (pos, reactivity)) in full_reactivity_data.iter().enumerate() { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_idx` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `idx` [INFO] [stdout] --> src/duet.rs:3445:10 [INFO] [stdout] | [INFO] [stdout] 3445 | for (idx, (pos, reactivity)) in non_full_reactivity_data.iter().enumerate() { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_idx` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/duet.rs:3743:9 [INFO] [stdout] | [INFO] [stdout] 3743 | let mut sigmas: Vec = knn_distances.iter().map(|dists| { [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `p` [INFO] [stdout] --> src/duet.rs:3708:9 [INFO] [stdout] | [INFO] [stdout] 3708 | let p = data[0].len(); [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_p` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/duet.rs:3830:9 [INFO] [stdout] | [INFO] [stdout] 3830 | let mut cluster_distances: Vec> = distances.clone(); [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `cluster_distances` [INFO] [stdout] --> src/duet.rs:3830:9 [INFO] [stdout] | [INFO] [stdout] 3830 | let mut cluster_distances: Vec> = distances.clone(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_cluster_distances` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/duet.rs:3890:9 [INFO] [stdout] | [INFO] [stdout] 3890 | let mut centered: Vec> = data.iter().map(|row| { [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `single_stranded_count` [INFO] [stdout] --> src/evaluate.rs:136:9 [INFO] [stdout] | [INFO] [stdout] 136 | let single_stranded_count = is_single_stranded.iter().filter(|&&x| x).count(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_single_stranded_count` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `double_stranded_count` [INFO] [stdout] --> src/evaluate.rs:137:9 [INFO] [stdout] | [INFO] [stdout] 137 | let double_stranded_count = is_single_stranded.iter().filter(|&&x| !x).count(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_double_stranded_count` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `total_lines` [INFO] [stdout] --> src/evaluate.rs:159:9 [INFO] [stdout] | [INFO] [stdout] 159 | let total_lines = std::fs::read_to_string(csv_file)?.lines().count(); [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_total_lines` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `match_rate` [INFO] [stdout] --> src/evaluate.rs:336:9 [INFO] [stdout] | [INFO] [stdout] 336 | let match_rate = if best_match_count > 0 { [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_match_rate` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `match_count` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:344:9 [INFO] [stdout] | [INFO] [stdout] 344 | let mut match_count = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_match_count` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `mismatch_count` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:345:9 [INFO] [stdout] | [INFO] [stdout] 345 | let mut mismatch_count = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_mismatch_count` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `skipped_count` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:346:9 [INFO] [stdout] | [INFO] [stdout] 346 | let mut skipped_count = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_skipped_count` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `match_count` is never read [INFO] [stdout] --> src/evaluate.rs:360:21 [INFO] [stdout] | [INFO] [stdout] 360 | match_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `mismatch_count` is never read [INFO] [stdout] --> src/evaluate.rs:362:21 [INFO] [stdout] | [INFO] [stdout] 362 | mismatch_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `skipped_count` is never read [INFO] [stdout] --> src/evaluate.rs:370:13 [INFO] [stdout] | [INFO] [stdout] 370 | skipped_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `skipped_count` is never read [INFO] [stdout] --> src/evaluate.rs:366:17 [INFO] [stdout] | [INFO] [stdout] 366 | skipped_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `thresholds` is never read [INFO] [stdout] --> src/evaluate.rs:624:26 [INFO] [stdout] | [INFO] [stdout] 624 | let mut thresholds = Vec::new(); [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `tn` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:1579:13 [INFO] [stdout] | [INFO] [stdout] 1579 | let mut tn = 0; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_tn` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `fn_count` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:1580:13 [INFO] [stdout] | [INFO] [stdout] 1580 | let mut fn_count = 0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_fn_count` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `tn` is never read [INFO] [stdout] --> src/evaluate.rs:1597:21 [INFO] [stdout] | [INFO] [stdout] 1597 | tn += 1; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `fn_count` is never read [INFO] [stdout] --> src/evaluate.rs:1595:21 [INFO] [stdout] | [INFO] [stdout] 1595 | fn_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `data` [INFO] [stdout] --> src/evaluate.rs:1839:16 [INFO] [stdout] | [INFO] [stdout] 1839 | for (base, data) in &base_groups { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_data` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `auc` [INFO] [stdout] --> src/evaluate.rs:1900:37 [INFO] [stdout] | [INFO] [stdout] 1900 | ... let auc = result.auc; [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_auc` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `signal_type` [INFO] [stdout] --> src/evaluate.rs:1952:5 [INFO] [stdout] | [INFO] [stdout] 1952 | signal_type: &str, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_signal_type` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `tn` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:2013:13 [INFO] [stdout] | [INFO] [stdout] 2013 | let mut tn = 0; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_tn` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `fn_count` is assigned to, but never used [INFO] [stdout] --> src/evaluate.rs:2014:13 [INFO] [stdout] | [INFO] [stdout] 2014 | let mut fn_count = 0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_fn_count` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `tn` is never read [INFO] [stdout] --> src/evaluate.rs:2031:21 [INFO] [stdout] | [INFO] [stdout] 2031 | tn += 1; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `fn_count` is never read [INFO] [stdout] --> src/evaluate.rs:2029:21 [INFO] [stdout] | [INFO] [stdout] 2029 | fn_count += 1; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_val` [INFO] [stdout] --> src/norm.rs:191:9 [INFO] [stdout] | [INFO] [stdout] 191 | let min_val = valid_values [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_val` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `logger` [INFO] [stdout] --> src/norm.rs:234:34 [INFO] [stdout] | [INFO] [stdout] 234 | pub fn norm_csv(args: &NormArgs, logger: &mut crate::Logger) -> Result<(), Box> { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_logger` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/norm.rs:510:9 [INFO] [stdout] | [INFO] [stdout] 510 | let mut window_start = 0; [INFO] [stdout] | ----^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `window_start` [INFO] [stdout] --> src/norm.rs:510:9 [INFO] [stdout] | [INFO] [stdout] 510 | let mut window_start = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_window_start` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `base_regex` [INFO] [stdout] --> src/plot.rs:99:9 [INFO] [stdout] | [INFO] [stdout] 99 | let base_regex = Regex::new(r"]*>([ATCGU])")?; [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_base_regex` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `skipped_lines` is assigned to, but never used [INFO] [stdout] --> src/plot.rs:283:9 [INFO] [stdout] | [INFO] [stdout] 283 | let mut skipped_lines = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_skipped_lines` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `total_lines` is assigned to, but never used [INFO] [stdout] --> src/plot.rs:284:9 [INFO] [stdout] | [INFO] [stdout] 284 | let mut total_lines = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_total_lines` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `skipped_lines` is never read [INFO] [stdout] --> src/plot.rs:295:13 [INFO] [stdout] | [INFO] [stdout] 295 | skipped_lines += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `total_lines` is never read [INFO] [stdout] --> src/plot.rs:290:9 [INFO] [stdout] | [INFO] [stdout] 290 | total_lines += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `written_lines` is assigned to, but never used [INFO] [stdout] --> src/plot.rs:316:9 [INFO] [stdout] | [INFO] [stdout] 316 | let mut written_lines = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_written_lines` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `written_lines` is never read [INFO] [stdout] --> src/plot.rs:330:13 [INFO] [stdout] | [INFO] [stdout] 330 | written_lines += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_pos2base` [INFO] [stdout] --> src/plot.rs:493:13 [INFO] [stdout] | [INFO] [stdout] 493 | let ref_pos2base = load_reference_sequence(ref_file)?; [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_pos2base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `is_stop_file` [INFO] [stdout] --> src/plot.rs:741:9 [INFO] [stdout] | [INFO] [stdout] 741 | let is_stop_file = csv_file.contains("stop"); [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_is_stop_file` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `is_mutation_file` [INFO] [stdout] --> src/plot.rs:742:9 [INFO] [stdout] | [INFO] [stdout] 742 | let is_mutation_file = csv_file.contains("mutation"); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_is_mutation_file` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reactivity_file` [INFO] [stdout] --> src/plot.rs:9018:5 [INFO] [stdout] | [INFO] [stdout] 9018 | reactivity_file: &str, [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reactivity_file` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `bases_filter` [INFO] [stdout] --> src/plot.rs:9021:5 [INFO] [stdout] | [INFO] [stdout] 9021 | bases_filter: &str, [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bases_filter` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `strand_filter` [INFO] [stdout] --> src/plot.rs:9023:5 [INFO] [stdout] | [INFO] [stdout] 9023 | strand_filter: &str, [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand_filter` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `id_regex` [INFO] [stdout] --> src/plot.rs:9101:9 [INFO] [stdout] | [INFO] [stdout] 9101 | let id_regex = Regex::new(r#"id="node_(\d+)""#)?; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_id_regex` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/progress.rs:85:29 [INFO] [stdout] | [INFO] [stdout] 85 | pub fn with_description(mut self, description: &str) -> io::Result<()> { [INFO] [stdout] | ----^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `best_threshold` is assigned to, but never used [INFO] [stdout] --> src/reactivity.rs:627:9 [INFO] [stdout] | [INFO] [stdout] 627 | let mut best_threshold = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_best_threshold` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_threshold` is never read [INFO] [stdout] --> src/reactivity.rs:666:13 [INFO] [stdout] | [INFO] [stdout] 666 | best_threshold = threshold; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `best_score_on_left` [INFO] [stdout] --> src/reactivity.rs:857:9 [INFO] [stdout] | [INFO] [stdout] 857 | let best_score_on_left = best_initial_k < 1.0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_best_score_on_left` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `best_coarse_auc` is assigned to, but never used [INFO] [stdout] --> src/reactivity.rs:893:9 [INFO] [stdout] | [INFO] [stdout] 893 | let mut best_coarse_auc = best_initial_auc; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_best_coarse_auc` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_score` is never read [INFO] [stdout] --> src/reactivity.rs:1002:13 [INFO] [stdout] | [INFO] [stdout] 1002 | best_coarse_score = score_left; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_score` is never read [INFO] [stdout] --> src/reactivity.rs:998:13 [INFO] [stdout] | [INFO] [stdout] 998 | best_coarse_score = score_right; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_score` is never read [INFO] [stdout] --> src/reactivity.rs:987:13 [INFO] [stdout] | [INFO] [stdout] 987 | best_coarse_score = score; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_score` is never read [INFO] [stdout] --> src/reactivity.rs:979:13 [INFO] [stdout] | [INFO] [stdout] 979 | best_coarse_score = score; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_auc` is never read [INFO] [stdout] --> src/reactivity.rs:1003:13 [INFO] [stdout] | [INFO] [stdout] 1003 | best_coarse_auc = auc_left; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_auc` is never read [INFO] [stdout] --> src/reactivity.rs:999:13 [INFO] [stdout] | [INFO] [stdout] 999 | best_coarse_auc = auc_right; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_auc` is never read [INFO] [stdout] --> src/reactivity.rs:988:13 [INFO] [stdout] | [INFO] [stdout] 988 | best_coarse_auc = auc; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `best_coarse_auc` is never read [INFO] [stdout] --> src/reactivity.rs:980:13 [INFO] [stdout] | [INFO] [stdout] 980 | best_coarse_auc = auc; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `df` [INFO] [stdout] --> src/main.rs:417:9 [INFO] [stdout] | [INFO] [stdout] 417 | let df = 2.0; [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_df` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `p` is never read [INFO] [stdout] --> src/main.rs:510:26 [INFO] [stdout] | [INFO] [stdout] 510 | let mut p: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `q` is never read [INFO] [stdout] --> src/main.rs:511:26 [INFO] [stdout] | [INFO] [stdout] 511 | let mut q: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `r` is never read [INFO] [stdout] --> src/main.rs:512:26 [INFO] [stdout] | [INFO] [stdout] 512 | let mut r: f64 = 0.0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `initial_params` [INFO] [stdout] --> src/main.rs:762:9 [INFO] [stdout] | [INFO] [stdout] 762 | let initial_params = vec![ [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_initial_params` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mutation_rate` [INFO] [stdout] --> src/main.rs:1202:5 [INFO] [stdout] | [INFO] [stdout] 1202 | mutation_rate: f64, [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mutation_rate` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `weight_decrease` [INFO] [stdout] --> src/main.rs:1206:5 [INFO] [stdout] | [INFO] [stdout] 1206 | weight_decrease: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_weight_decrease` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:1466:9 [INFO] [stdout] | [INFO] [stdout] 1466 | let mut expected_refs: HashSet = region_intervals.keys().cloned().collect(); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `num_threads` [INFO] [stdout] --> src/main.rs:1436:5 [INFO] [stdout] | [INFO] [stdout] 1436 | num_threads: usize, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_num_threads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `base_recommendation` [INFO] [stdout] --> src/main.rs:2950:9 [INFO] [stdout] | [INFO] [stdout] 2950 | let base_recommendation = (bam_file_count * 2).min(64); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_base_recommendation` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `completed` [INFO] [stdout] --> src/main.rs:3095:9 [INFO] [stdout] | [INFO] [stdout] 3095 | let completed = Arc::new(AtomicUsize::new(0)); [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_completed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_seq` [INFO] [stdout] --> src/main.rs:3359:24 [INFO] [stdout] | [INFO] [stdout] 3359 | for (ref_name, ref_seq) in &reference_sequences { [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_seq` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_name` [INFO] [stdout] --> src/main.rs:3727:10 [INFO] [stdout] | [INFO] [stdout] 3727 | for (ref_name, intervals) in &distribution { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_name` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_base` [INFO] [stdout] --> src/main.rs:3996:21 [INFO] [stdout] | [INFO] [stdout] 3996 | let ref_base = if pos < ref_seq.len() as u32 { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/main.rs:4444:9 [INFO] [stdout] | [INFO] [stdout] 4444 | let header = bam.header().to_owned(); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `PositionData` is more private than the item `ReplicateData::replicates` [INFO] [stdout] --> src/compare.rs:54:5 [INFO] [stdout] | [INFO] [stdout] 54 | pub replicates: Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ field `ReplicateData::replicates` is reachable at visibility `pub(crate)` [INFO] [stdout] | [INFO] [stdout] note: but type `PositionData` is only usable at visibility `pub(self)` [INFO] [stdout] --> src/compare.rs:110:1 [INFO] [stdout] | [INFO] [stdout] 110 | struct PositionData { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = note: `#[warn(private_interfaces)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `tid` is never read [INFO] [stdout] --> src/main.rs:398:5 [INFO] [stdout] | [INFO] [stdout] 397 | struct Item { [INFO] [stdout] | ---- field in this struct [INFO] [stdout] 398 | tid: String, [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Item` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `normalize_signal` is never used [INFO] [stdout] --> src/main.rs:1608:4 [INFO] [stdout] | [INFO] [stdout] 1608 | fn normalize_signal( [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: enum `CompareMode` is never used [INFO] [stdout] --> src/compare.rs:12:10 [INFO] [stdout] | [INFO] [stdout] 12 | pub enum CompareMode { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `test_type` is never read [INFO] [stdout] --> src/compare.rs:43:9 [INFO] [stdout] | [INFO] [stdout] 42 | pub struct StatisticalResult { [INFO] [stdout] | ----------------- field in this struct [INFO] [stdout] 43 | pub test_type: StatisticalTest, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `StatisticalResult` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `ReplicateData` is never constructed [INFO] [stdout] --> src/compare.rs:52:12 [INFO] [stdout] | [INFO] [stdout] 52 | pub struct ReplicateData { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `ComparisonResult` is never constructed [INFO] [stdout] --> src/compare.rs:59:12 [INFO] [stdout] | [INFO] [stdout] 59 | pub struct ComparisonResult { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `DiffScanResult` is never constructed [INFO] [stdout] --> src/compare.rs:73:12 [INFO] [stdout] | [INFO] [stdout] 73 | pub struct DiffScanResult { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `DeltaSHAPEResult` is never constructed [INFO] [stdout] --> src/compare.rs:89:12 [INFO] [stdout] | [INFO] [stdout] 89 | pub struct DeltaSHAPEResult { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `NormalizationParams` is never constructed [INFO] [stdout] --> src/compare.rs:104:12 [INFO] [stdout] | [INFO] [stdout] 104 | pub struct NormalizationParams { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `ins`, `del`, `a`, `c`, `g`, and `t` are never read [INFO] [stdout] --> src/compare.rs:118:5 [INFO] [stdout] | [INFO] [stdout] 110 | struct PositionData { [INFO] [stdout] | ------------ fields in this struct [INFO] [stdout] ... [INFO] [stdout] 118 | ins: usize, [INFO] [stdout] | ^^^ [INFO] [stdout] 119 | del: usize, [INFO] [stdout] | ^^^ [INFO] [stdout] 120 | a: u32, [INFO] [stdout] | ^ [INFO] [stdout] 121 | c: u32, [INFO] [stdout] | ^ [INFO] [stdout] 122 | g: u32, [INFO] [stdout] | ^ [INFO] [stdout] 123 | t: u32, [INFO] [stdout] | ^ [INFO] [stdout] | [INFO] [stdout] = note: `PositionData` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `normalize_reactivity_data` is never used [INFO] [stdout] --> src/compare.rs:437:4 [INFO] [stdout] | [INFO] [stdout] 437 | fn normalize_reactivity_data( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `quantile_normalization` is never used [INFO] [stdout] --> src/compare.rs:451:4 [INFO] [stdout] | [INFO] [stdout] 451 | fn quantile_normalization( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `robust_normalization` is never used [INFO] [stdout] --> src/compare.rs:500:4 [INFO] [stdout] | [INFO] [stdout] 500 | fn robust_normalization( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `median_normalization` is never used [INFO] [stdout] --> src/compare.rs:535:4 [INFO] [stdout] | [INFO] [stdout] 535 | fn median_normalization( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_mad` is never used [INFO] [stdout] --> src/compare.rs:575:4 [INFO] [stdout] | [INFO] [stdout] 575 | fn calculate_mad(values: &[f64], median: f64) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compare_samples` is never used [INFO] [stdout] --> src/compare.rs:1764:8 [INFO] [stdout] | [INFO] [stdout] 1764 | pub fn compare_samples( [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_reference_sequence` is never used [INFO] [stdout] --> src/convert.rs:372:4 [INFO] [stdout] | [INFO] [stdout] 372 | fn load_reference_sequence(fasta_path: &str, chr_name: Option<&str>) -> Result, Box> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `MIN_SHARED_FRACTION` is never used [INFO] [stdout] --> src/duet.rs:29:7 [INFO] [stdout] | [INFO] [stdout] 29 | const MIN_SHARED_FRACTION: f64 = 0.15; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `MIN_REACTIVITY_CORRELATION` is never used [INFO] [stdout] --> src/duet.rs:33:7 [INFO] [stdout] | [INFO] [stdout] 33 | const MIN_REACTIVITY_CORRELATION: f64 = 0.60; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `plot_single_track` is never used [INFO] [stdout] --> src/duet.rs:3555:4 [INFO] [stdout] | [INFO] [stdout] 3555 | fn plot_single_track( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `ReactivityData` is never constructed [INFO] [stdout] --> src/norm.rs:97:8 [INFO] [stdout] | [INFO] [stdout] 97 | struct ReactivityData { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `dynamic_window_norm` is never used [INFO] [stdout] --> src/norm.rs:475:4 [INFO] [stdout] | [INFO] [stdout] 475 | fn dynamic_window_norm( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_adaptive_window` is never used [INFO] [stdout] --> src/norm.rs:581:4 [INFO] [stdout] | [INFO] [stdout] 581 | fn find_adaptive_window( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_dynamic_window` is never used [INFO] [stdout] --> src/norm.rs:620:4 [INFO] [stdout] | [INFO] [stdout] 620 | fn find_dynamic_window( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `normalize_window` is never used [INFO] [stdout] --> src/norm.rs:630:4 [INFO] [stdout] | [INFO] [stdout] 630 | fn normalize_window(values: &[f64], norm_method: &StopNormMethod) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `SvgElement` is never constructed [INFO] [stdout] --> src/plot.rs:75:12 [INFO] [stdout] | [INFO] [stdout] 75 | pub struct SvgElement { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `is_high` is never read [INFO] [stdout] --> src/plot.rs:663:5 [INFO] [stdout] | [INFO] [stdout] 657 | struct GenePlotTask { [INFO] [stdout] | ------------ field in this struct [INFO] [stdout] ... [INFO] [stdout] 663 | is_high: bool, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `GenePlotTask` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `gene_id` and `cov_x_depth` are never read [INFO] [stdout] --> src/plot.rs:668:5 [INFO] [stdout] | [INFO] [stdout] 667 | struct GeneStat { [INFO] [stdout] | -------- fields in this struct [INFO] [stdout] 668 | gene_id: String, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 671 | cov_x_depth: f64, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `GeneStat` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_best_shift_for_base` is never used [INFO] [stdout] --> src/plot.rs:2155:8 [INFO] [stdout] | [INFO] [stdout] 2155 | pub fn find_best_shift_for_base( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `ProgressBar` is never constructed [INFO] [stdout] --> src/progress.rs:4:12 [INFO] [stdout] | [INFO] [stdout] 4 | pub struct ProgressBar { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `with_width`, `update`, `display`, `finish`, and `with_description` are never used [INFO] [stdout] --> src/progress.rs:13:12 [INFO] [stdout] | [INFO] [stdout] 11 | impl ProgressBar { [INFO] [stdout] | ---------------- associated items in this implementation [INFO] [stdout] 12 | /// Create a new progress bar [INFO] [stdout] 13 | pub fn new(total: usize) -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 23 | pub fn with_width(mut self, width: usize) -> Self { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 29 | pub fn update(&mut self, current: usize) -> io::Result<()> { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 47 | fn display(&self) -> io::Result<()> { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 77 | pub fn finish(&mut self) -> io::Result<()> { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 85 | pub fn with_description(mut self, description: &str) -> io::Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `DescriptiveProgress` is never constructed [INFO] [stdout] --> src/progress.rs:162:12 [INFO] [stdout] | [INFO] [stdout] 162 | pub struct DescriptiveProgress { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `update`, and `finish` are never used [INFO] [stdout] --> src/progress.rs:171:12 [INFO] [stdout] | [INFO] [stdout] 169 | impl DescriptiveProgress { [INFO] [stdout] | ------------------------ associated items in this implementation [INFO] [stdout] 170 | /// Create a new descriptive progress displayer [INFO] [stdout] 171 | pub fn new(total: usize, description: &str) -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 181 | pub fn update(&mut self, current: usize) -> io::Result<()> { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 203 | pub fn finish(&mut self) -> io::Result<()> { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `vs_low_p50`, `vs_overall_p50`, and `correction_p50` are never read [INFO] [stdout] --> src/reactivity.rs:270:5 [INFO] [stdout] | [INFO] [stdout] 267 | struct DistributionTargets { [INFO] [stdout] | ------------------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 270 | vs_low_p50: f64, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 277 | vs_overall_p50: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 284 | correction_p50: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_auc_for_k` is never used [INFO] [stdout] --> src/reactivity.rs:713:4 [INFO] [stdout] | [INFO] [stdout] 713 | fn calculate_auc_for_k( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:1442:5 [INFO] [stdout] | [INFO] [stdout] 1442 | bam.set_threads(1); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] = note: `#[warn(unused_must_use)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 1442 | let _ = bam.set_threads(1); [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:3493:13 [INFO] [stdout] | [INFO] [stdout] 3493 | bam.set_threads(1); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 3493 | let _ = bam.set_threads(1); [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:4442:5 [INFO] [stdout] | [INFO] [stdout] 4442 | bam.set_threads(1); // Avoid internal multi-threading conflicts [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 4442 | let _ = bam.set_threads(1); // Avoid internal multi-threading conflicts [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:4475:9 [INFO] [stdout] | [INFO] [stdout] 4475 | window_bam.set_threads(1); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 4475 | let _ = window_bam.set_threads(1); [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: comparison is useless due to type limits [INFO] [stdout] --> src/main.rs:4549:32 [INFO] [stdout] | [INFO] [stdout] 4549 | ... if qpos >= 0 && (qpos as usize) < quals.len() { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_comparisons)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compute_scan_Q` should have a snake case name [INFO] [stdout] --> src/compare.rs:274:4 [INFO] [stdout] | [INFO] [stdout] 274 | fn compute_scan_Q( [INFO] [stdout] | ^^^^^^^^^^^^^^ help: convert the identifier to snake case: `compute_scan_q` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 5.16s [INFO] running `Command { std: "docker" "inspect" "78eb208184dae26e70eb02a5ac11d1aa2c32d95b51d4f7b8293eaeb96dae4cfc", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "78eb208184dae26e70eb02a5ac11d1aa2c32d95b51d4f7b8293eaeb96dae4cfc", kill_on_drop: false }` [INFO] [stdout] 78eb208184dae26e70eb02a5ac11d1aa2c32d95b51d4f7b8293eaeb96dae4cfc [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+d933cf483edf1605142ac6899ff32536c0ad8b22" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 9b0f875c99da72010dbd65b2a40abab1ae13ec0e63398786192b2a3fc052f797 [INFO] running `Command { std: "docker" "start" "-a" "9b0f875c99da72010dbd65b2a40abab1ae13ec0e63398786192b2a3fc052f797", kill_on_drop: false }` [INFO] [stderr] warning: unused imports: `AtomicUsize` and `Ordering` [INFO] [stderr] --> src/main.rs:14:25 [INFO] [stderr] | [INFO] [stderr] 14 | use std::sync::atomic::{AtomicUsize, Ordering}; [INFO] [stderr] | ^^^^^^^^^^^ ^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::sync::Arc` [INFO] [stderr] --> src/main.rs:15:5 [INFO] [stderr] | [INFO] [stderr] 15 | use std::sync::Arc; [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `Array1` and `Array2` [INFO] [stderr] --> src/main.rs:22:15 [INFO] [stderr] | [INFO] [stderr] 22 | use ndarray::{Array1, Array2}; [INFO] [stderr] | ^^^^^^ ^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::collections::HashMap` [INFO] [stderr] --> src/convert.rs:1313:9 [INFO] [stderr] | [INFO] [stderr] 1313 | use std::collections::HashMap; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::collections::HashMap` [INFO] [stderr] --> src/correct.rs:4:5 [INFO] [stderr] | [INFO] [stderr] 4 | use std::collections::HashMap; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unnecessary parentheses around function argument [INFO] [stderr] --> src/duet.rs:2823:21 [INFO] [stderr] | [INFO] [stderr] 2823 | ((165.0 * (1.0 - t)) as u8), [INFO] [stderr] | ^ ^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] help: remove these parentheses [INFO] [stderr] | [INFO] [stderr] 2823 - ((165.0 * (1.0 - t)) as u8), [INFO] [stderr] 2823 + (165.0 * (1.0 - t)) as u8 , [INFO] [stderr] | [INFO] [stderr] [INFO] [stderr] warning: unnecessary parentheses around function argument [INFO] [stderr] --> src/duet.rs:2866:17 [INFO] [stderr] | [INFO] [stderr] 2866 | ((165.0 * (1.0 - t)) as u8), [INFO] [stderr] | ^ ^ [INFO] [stderr] | [INFO] [stderr] help: remove these parentheses [INFO] [stderr] | [INFO] [stderr] 2866 - ((165.0 * (1.0 - t)) as u8), [INFO] [stderr] 2866 + (165.0 * (1.0 - t)) as u8 , [INFO] [stderr] | [INFO] [stderr] [INFO] [stderr] warning: unused import: `Read` [INFO] [stderr] --> src/reactivity.rs:7:42 [INFO] [stderr] | [INFO] [stderr] 7 | use std::io::{BufRead, BufReader, Write, Read}; [INFO] [stderr] | ^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused variable: `n` [INFO] [stderr] --> src/compare.rs:325:9 [INFO] [stderr] | [INFO] [stderr] 325 | let n = base.len(); [INFO] [stderr] | ^ help: if this is intentional, prefix it with an underscore: `_n` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/compare.rs:391:13 [INFO] [stderr] | [INFO] [stderr] 391 | let mut region_start = i; [INFO] [stderr] | ----^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `window_radius` [INFO] [stderr] --> src/compare.rs:355:5 [INFO] [stderr] | [INFO] [stderr] 355 | window_radius: usize, [INFO] [stderr] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_window_radius` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/convert.rs:867:28 [INFO] [stderr] | [INFO] [stderr] 867 | let (mut ref_base, mut mutation_count, mut rt_stops, mut coverage) = [INFO] [stderr] | ----^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `args` [INFO] [stderr] --> src/convert.rs:1052:5 [INFO] [stderr] | [INFO] [stderr] 1052 | args: &ConvertArgs, [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_args` [INFO] [stderr] [INFO] [stderr] warning: variable `in_transcript` is assigned to, but never used [INFO] [stderr] --> src/convert.rs:1204:9 [INFO] [stderr] | [INFO] [stderr] 1204 | let mut in_transcript = false; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_in_transcript` instead [INFO] [stderr] [INFO] [stderr] warning: value assigned to `in_transcript` is never read [INFO] [stderr] --> src/convert.rs:1214:25 [INFO] [stderr] | [INFO] [stderr] 1214 | in_transcript = true; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: value assigned to `in_transcript` is never read [INFO] [stderr] --> src/convert.rs:1246:25 [INFO] [stderr] | [INFO] [stderr] 1246 | in_transcript = false; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/convert.rs:1858:9 [INFO] [stderr] | [INFO] [stderr] 1858 | let mut line_iter = reader.lines(); [INFO] [stderr] | ----^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `key` [INFO] [stderr] --> src/convert.rs:2095:10 [INFO] [stderr] | [INFO] [stderr] 2095 | for (key, mut entries) in entries_by_key { [INFO] [stderr] | ^^^ help: if this is intentional, prefix it with an underscore: `_key` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `df` [INFO] [stderr] --> src/correct.rs:32:9 [INFO] [stderr] | [INFO] [stderr] 32 | let df = 2.0; [INFO] [stderr] | ^^ help: if this is intentional, prefix it with an underscore: `_df` [INFO] [stderr] [INFO] [stderr] warning: value assigned to `p` is never read [INFO] [stderr] --> src/correct.rs:122:26 [INFO] [stderr] | [INFO] [stderr] 122 | let mut p: f64 = 0.0; [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `q` is never read [INFO] [stderr] --> src/correct.rs:123:26 [INFO] [stderr] | [INFO] [stderr] 123 | let mut q: f64 = 0.0; [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `r` is never read [INFO] [stderr] --> src/correct.rs:124:26 [INFO] [stderr] | [INFO] [stderr] 124 | let mut r: f64 = 0.0; [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: unused variable: `max_mutation` [INFO] [stderr] --> src/correct.rs:344:9 [INFO] [stderr] | [INFO] [stderr] 344 | let max_mutation = binned.iter().map(|(_, mr)| *mr).fold(0.0, f64::max); [INFO] [stderr] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_mutation` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `mutation_rate` [INFO] [stderr] --> src/correct.rs:394:5 [INFO] [stderr] | [INFO] [stderr] 394 | mutation_rate: f64, [INFO] [stderr] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mutation_rate` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `weight_decrease` [INFO] [stderr] --> src/correct.rs:398:5 [INFO] [stderr] | [INFO] [stderr] 398 | weight_decrease: f64, [INFO] [stderr] | ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_weight_decrease` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/duet.rs:2697:9 [INFO] [stderr] | [INFO] [stderr] 2697 | let mut reordered_ensemble_ids: Vec = row_order.iter().map(|&idx| ensemble_ids[idx]).collect(); [INFO] [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/duet.rs:2698:9 [INFO] [stderr] | [INFO] [stderr] 2698 | let mut reordered_matrix: Vec> = row_order.iter().map(|&idx| reactivity_matrix[idx].clone()).collect(); [INFO] [stderr] | ----^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `base_plot_height` [INFO] [stderr] --> src/duet.rs:2724:9 [INFO] [stderr] | [INFO] [stderr] 2724 | let base_plot_height = 800; [INFO] [stderr] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_base_plot_height` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `ensemble` [INFO] [stderr] --> src/duet.rs:3033:21 [INFO] [stderr] | [INFO] [stderr] 3033 | if let Some(ensemble) = global_ensembles.iter().find(|e| e.id == ensemble_id) { [INFO] [stderr] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ensemble` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `range` [INFO] [stderr] --> src/duet.rs:3244:21 [INFO] [stderr] | [INFO] [stderr] 3244 | let range = max_pos - min_pos; [INFO] [stderr] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_range` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `idx` [INFO] [stderr] --> src/duet.rs:3417:10 [INFO] [stderr] | [INFO] [stderr] 3417 | for (idx, (pos, reactivity)) in full_reactivity_data.iter().enumerate() { [INFO] [stderr] | ^^^ help: if this is intentional, prefix it with an underscore: `_idx` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `idx` [INFO] [stderr] --> src/duet.rs:3445:10 [INFO] [stderr] | [INFO] [stderr] 3445 | for (idx, (pos, reactivity)) in non_full_reactivity_data.iter().enumerate() { [INFO] [stderr] | ^^^ help: if this is intentional, prefix it with an underscore: `_idx` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/duet.rs:3743:9 [INFO] [stderr] | [INFO] [stderr] 3743 | let mut sigmas: Vec = knn_distances.iter().map(|dists| { [INFO] [stderr] | ----^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `p` [INFO] [stderr] --> src/duet.rs:3708:9 [INFO] [stderr] | [INFO] [stderr] 3708 | let p = data[0].len(); [INFO] [stderr] | ^ help: if this is intentional, prefix it with an underscore: `_p` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/duet.rs:3830:9 [INFO] [stderr] | [INFO] [stderr] 3830 | let mut cluster_distances: Vec> = distances.clone(); [INFO] [stderr] | ----^^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `cluster_distances` [INFO] [stderr] --> src/duet.rs:3830:9 [INFO] [stderr] | [INFO] [stderr] 3830 | let mut cluster_distances: Vec> = distances.clone(); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_cluster_distances` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/duet.rs:3890:9 [INFO] [stderr] | [INFO] [stderr] 3890 | let mut centered: Vec> = data.iter().map(|row| { [INFO] [stderr] | ----^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `single_stranded_count` [INFO] [stderr] --> src/evaluate.rs:136:9 [INFO] [stderr] | [INFO] [stderr] 136 | let single_stranded_count = is_single_stranded.iter().filter(|&&x| x).count(); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_single_stranded_count` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `double_stranded_count` [INFO] [stderr] --> src/evaluate.rs:137:9 [INFO] [stderr] | [INFO] [stderr] 137 | let double_stranded_count = is_single_stranded.iter().filter(|&&x| !x).count(); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_double_stranded_count` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `total_lines` [INFO] [stderr] --> src/evaluate.rs:159:9 [INFO] [stderr] | [INFO] [stderr] 159 | let total_lines = std::fs::read_to_string(csv_file)?.lines().count(); [INFO] [stderr] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_total_lines` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `match_rate` [INFO] [stderr] --> src/evaluate.rs:336:9 [INFO] [stderr] | [INFO] [stderr] 336 | let match_rate = if best_match_count > 0 { [INFO] [stderr] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_match_rate` [INFO] [stderr] [INFO] [stderr] warning: variable `match_count` is assigned to, but never used [INFO] [stderr] --> src/evaluate.rs:344:9 [INFO] [stderr] | [INFO] [stderr] 344 | let mut match_count = 0; [INFO] [stderr] | ^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_match_count` instead [INFO] [stderr] [INFO] [stderr] warning: variable `mismatch_count` is assigned to, but never used [INFO] [stderr] --> src/evaluate.rs:345:9 [INFO] [stderr] | [INFO] [stderr] 345 | let mut mismatch_count = 0; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_mismatch_count` instead [INFO] [stderr] [INFO] [stderr] warning: variable `skipped_count` is assigned to, but never used [INFO] [stderr] --> src/evaluate.rs:346:9 [INFO] [stderr] | [INFO] [stderr] 346 | let mut skipped_count = 0; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_skipped_count` instead [INFO] [stderr] [INFO] [stderr] warning: value assigned to `match_count` is never read [INFO] [stderr] --> src/evaluate.rs:360:21 [INFO] [stderr] | [INFO] [stderr] 360 | match_count += 1; [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `mismatch_count` is never read [INFO] [stderr] --> src/evaluate.rs:362:21 [INFO] [stderr] | [INFO] [stderr] 362 | mismatch_count += 1; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `skipped_count` is never read [INFO] [stderr] --> src/evaluate.rs:370:13 [INFO] [stderr] | [INFO] [stderr] 370 | skipped_count += 1; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `skipped_count` is never read [INFO] [stderr] --> src/evaluate.rs:366:17 [INFO] [stderr] | [INFO] [stderr] 366 | skipped_count += 1; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `thresholds` is never read [INFO] [stderr] --> src/evaluate.rs:624:26 [INFO] [stderr] | [INFO] [stderr] 624 | let mut thresholds = Vec::new(); [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: variable `tn` is assigned to, but never used [INFO] [stderr] --> src/evaluate.rs:1579:13 [INFO] [stderr] | [INFO] [stderr] 1579 | let mut tn = 0; [INFO] [stderr] | ^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_tn` instead [INFO] [stderr] [INFO] [stderr] warning: variable `fn_count` is assigned to, but never used [INFO] [stderr] --> src/evaluate.rs:1580:13 [INFO] [stderr] | [INFO] [stderr] 1580 | let mut fn_count = 0; [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_fn_count` instead [INFO] [stderr] [INFO] [stderr] warning: value assigned to `tn` is never read [INFO] [stderr] --> src/evaluate.rs:1597:21 [INFO] [stderr] | [INFO] [stderr] 1597 | tn += 1; [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `fn_count` is never read [INFO] [stderr] --> src/evaluate.rs:1595:21 [INFO] [stderr] | [INFO] [stderr] 1595 | fn_count += 1; [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: unused variable: `data` [INFO] [stderr] --> src/evaluate.rs:1839:16 [INFO] [stderr] | [INFO] [stderr] 1839 | for (base, data) in &base_groups { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_data` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `auc` [INFO] [stderr] --> src/evaluate.rs:1900:37 [INFO] [stderr] | [INFO] [stderr] 1900 | ... let auc = result.auc; [INFO] [stderr] | ^^^ help: if this is intentional, prefix it with an underscore: `_auc` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `signal_type` [INFO] [stderr] --> src/evaluate.rs:1952:5 [INFO] [stderr] | [INFO] [stderr] 1952 | signal_type: &str, [INFO] [stderr] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_signal_type` [INFO] [stderr] [INFO] [stderr] warning: variable `tn` is assigned to, but never used [INFO] [stderr] --> src/evaluate.rs:2013:13 [INFO] [stderr] | [INFO] [stderr] 2013 | let mut tn = 0; [INFO] [stderr] | ^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_tn` instead [INFO] [stderr] [INFO] [stderr] warning: variable `fn_count` is assigned to, but never used [INFO] [stderr] --> src/evaluate.rs:2014:13 [INFO] [stderr] | [INFO] [stderr] 2014 | let mut fn_count = 0; [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_fn_count` instead [INFO] [stderr] [INFO] [stderr] warning: value assigned to `tn` is never read [INFO] [stderr] --> src/evaluate.rs:2031:21 [INFO] [stderr] | [INFO] [stderr] 2031 | tn += 1; [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `fn_count` is never read [INFO] [stderr] --> src/evaluate.rs:2029:21 [INFO] [stderr] | [INFO] [stderr] 2029 | fn_count += 1; [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: unused variable: `min_val` [INFO] [stderr] --> src/norm.rs:191:9 [INFO] [stderr] | [INFO] [stderr] 191 | let min_val = valid_values [INFO] [stderr] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_val` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `logger` [INFO] [stderr] --> src/norm.rs:234:34 [INFO] [stderr] | [INFO] [stderr] 234 | pub fn norm_csv(args: &NormArgs, logger: &mut crate::Logger) -> Result<(), Box> { [INFO] [stderr] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_logger` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/norm.rs:510:9 [INFO] [stderr] | [INFO] [stderr] 510 | let mut window_start = 0; [INFO] [stderr] | ----^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `window_start` [INFO] [stderr] --> src/norm.rs:510:9 [INFO] [stderr] | [INFO] [stderr] 510 | let mut window_start = 0; [INFO] [stderr] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_window_start` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `base_regex` [INFO] [stderr] --> src/plot.rs:99:9 [INFO] [stderr] | [INFO] [stderr] 99 | let base_regex = Regex::new(r"]*>([ATCGU])")?; [INFO] [stderr] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_base_regex` [INFO] [stderr] [INFO] [stderr] warning: variable `skipped_lines` is assigned to, but never used [INFO] [stderr] --> src/plot.rs:283:9 [INFO] [stderr] | [INFO] [stderr] 283 | let mut skipped_lines = 0; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_skipped_lines` instead [INFO] [stderr] [INFO] [stderr] warning: variable `total_lines` is assigned to, but never used [INFO] [stderr] --> src/plot.rs:284:9 [INFO] [stderr] | [INFO] [stderr] 284 | let mut total_lines = 0; [INFO] [stderr] | ^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_total_lines` instead [INFO] [stderr] [INFO] [stderr] warning: value assigned to `skipped_lines` is never read [INFO] [stderr] --> src/plot.rs:295:13 [INFO] [stderr] | [INFO] [stderr] 295 | skipped_lines += 1; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `total_lines` is never read [INFO] [stderr] --> src/plot.rs:290:9 [INFO] [stderr] | [INFO] [stderr] 290 | total_lines += 1; [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: variable `written_lines` is assigned to, but never used [INFO] [stderr] --> src/plot.rs:316:9 [INFO] [stderr] | [INFO] [stderr] 316 | let mut written_lines = 0; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_written_lines` instead [INFO] [stderr] [INFO] [stderr] warning: value assigned to `written_lines` is never read [INFO] [stderr] --> src/plot.rs:330:13 [INFO] [stderr] | [INFO] [stderr] 330 | written_lines += 1; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: unused variable: `ref_pos2base` [INFO] [stderr] --> src/plot.rs:493:13 [INFO] [stderr] | [INFO] [stderr] 493 | let ref_pos2base = load_reference_sequence(ref_file)?; [INFO] [stderr] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_pos2base` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `is_stop_file` [INFO] [stderr] --> src/plot.rs:741:9 [INFO] [stderr] | [INFO] [stderr] 741 | let is_stop_file = csv_file.contains("stop"); [INFO] [stderr] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_is_stop_file` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `is_mutation_file` [INFO] [stderr] --> src/plot.rs:742:9 [INFO] [stderr] | [INFO] [stderr] 742 | let is_mutation_file = csv_file.contains("mutation"); [INFO] [stderr] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_is_mutation_file` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `reactivity_file` [INFO] [stderr] --> src/plot.rs:9018:5 [INFO] [stderr] | [INFO] [stderr] 9018 | reactivity_file: &str, [INFO] [stderr] | ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reactivity_file` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `bases_filter` [INFO] [stderr] --> src/plot.rs:9021:5 [INFO] [stderr] | [INFO] [stderr] 9021 | bases_filter: &str, [INFO] [stderr] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bases_filter` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `strand_filter` [INFO] [stderr] --> src/plot.rs:9023:5 [INFO] [stderr] | [INFO] [stderr] 9023 | strand_filter: &str, [INFO] [stderr] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand_filter` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `id_regex` [INFO] [stderr] --> src/plot.rs:9101:9 [INFO] [stderr] | [INFO] [stderr] 9101 | let id_regex = Regex::new(r#"id="node_(\d+)""#)?; [INFO] [stderr] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_id_regex` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/progress.rs:85:29 [INFO] [stderr] | [INFO] [stderr] 85 | pub fn with_description(mut self, description: &str) -> io::Result<()> { [INFO] [stderr] | ----^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable `best_threshold` is assigned to, but never used [INFO] [stderr] --> src/reactivity.rs:627:9 [INFO] [stderr] | [INFO] [stderr] 627 | let mut best_threshold = 0.0; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_best_threshold` instead [INFO] [stderr] [INFO] [stderr] warning: value assigned to `best_threshold` is never read [INFO] [stderr] --> src/reactivity.rs:666:13 [INFO] [stderr] | [INFO] [stderr] 666 | best_threshold = threshold; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: unused variable: `best_score_on_left` [INFO] [stderr] --> src/reactivity.rs:857:9 [INFO] [stderr] | [INFO] [stderr] 857 | let best_score_on_left = best_initial_k < 1.0; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_best_score_on_left` [INFO] [stderr] [INFO] [stderr] warning: variable `best_coarse_auc` is assigned to, but never used [INFO] [stderr] --> src/reactivity.rs:893:9 [INFO] [stderr] | [INFO] [stderr] 893 | let mut best_coarse_auc = best_initial_auc; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: consider using `_best_coarse_auc` instead [INFO] [stderr] [INFO] [stderr] warning: value assigned to `best_coarse_score` is never read [INFO] [stderr] --> src/reactivity.rs:1002:13 [INFO] [stderr] | [INFO] [stderr] 1002 | best_coarse_score = score_left; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `best_coarse_score` is never read [INFO] [stderr] --> src/reactivity.rs:998:13 [INFO] [stderr] | [INFO] [stderr] 998 | best_coarse_score = score_right; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `best_coarse_score` is never read [INFO] [stderr] --> src/reactivity.rs:987:13 [INFO] [stderr] | [INFO] [stderr] 987 | best_coarse_score = score; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `best_coarse_score` is never read [INFO] [stderr] --> src/reactivity.rs:979:13 [INFO] [stderr] | [INFO] [stderr] 979 | best_coarse_score = score; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `best_coarse_auc` is never read [INFO] [stderr] --> src/reactivity.rs:1003:13 [INFO] [stderr] | [INFO] [stderr] 1003 | best_coarse_auc = auc_left; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `best_coarse_auc` is never read [INFO] [stderr] --> src/reactivity.rs:999:13 [INFO] [stderr] | [INFO] [stderr] 999 | best_coarse_auc = auc_right; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `best_coarse_auc` is never read [INFO] [stderr] --> src/reactivity.rs:988:13 [INFO] [stderr] | [INFO] [stderr] 988 | best_coarse_auc = auc; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `best_coarse_auc` is never read [INFO] [stderr] --> src/reactivity.rs:980:13 [INFO] [stderr] | [INFO] [stderr] 980 | best_coarse_auc = auc; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: unused variable: `df` [INFO] [stderr] --> src/main.rs:417:9 [INFO] [stderr] | [INFO] [stderr] 417 | let df = 2.0; [INFO] [stderr] | ^^ help: if this is intentional, prefix it with an underscore: `_df` [INFO] [stderr] [INFO] [stderr] warning: value assigned to `p` is never read [INFO] [stderr] --> src/main.rs:510:26 [INFO] [stderr] | [INFO] [stderr] 510 | let mut p: f64 = 0.0; [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `q` is never read [INFO] [stderr] --> src/main.rs:511:26 [INFO] [stderr] | [INFO] [stderr] 511 | let mut q: f64 = 0.0; [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: value assigned to `r` is never read [INFO] [stderr] --> src/main.rs:512:26 [INFO] [stderr] | [INFO] [stderr] 512 | let mut r: f64 = 0.0; [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] [INFO] [stderr] warning: unused variable: `initial_params` [INFO] [stderr] --> src/main.rs:762:9 [INFO] [stderr] | [INFO] [stderr] 762 | let initial_params = vec![ [INFO] [stderr] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_initial_params` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `mutation_rate` [INFO] [stderr] --> src/main.rs:1202:5 [INFO] [stderr] | [INFO] [stderr] 1202 | mutation_rate: f64, [INFO] [stderr] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mutation_rate` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `weight_decrease` [INFO] [stderr] --> src/main.rs:1206:5 [INFO] [stderr] | [INFO] [stderr] 1206 | weight_decrease: f64, [INFO] [stderr] | ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_weight_decrease` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/main.rs:1466:9 [INFO] [stderr] | [INFO] [stderr] 1466 | let mut expected_refs: HashSet = region_intervals.keys().cloned().collect(); [INFO] [stderr] | ----^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `num_threads` [INFO] [stderr] --> src/main.rs:1436:5 [INFO] [stderr] | [INFO] [stderr] 1436 | num_threads: usize, [INFO] [stderr] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_num_threads` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `base_recommendation` [INFO] [stderr] --> src/main.rs:2950:9 [INFO] [stderr] | [INFO] [stderr] 2950 | let base_recommendation = (bam_file_count * 2).min(64); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_base_recommendation` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `completed` [INFO] [stderr] --> src/main.rs:3095:9 [INFO] [stderr] | [INFO] [stderr] 3095 | let completed = Arc::new(AtomicUsize::new(0)); [INFO] [stderr] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_completed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `ref_seq` [INFO] [stderr] --> src/main.rs:3359:24 [INFO] [stderr] | [INFO] [stderr] 3359 | for (ref_name, ref_seq) in &reference_sequences { [INFO] [stderr] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_seq` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `ref_name` [INFO] [stderr] --> src/main.rs:3727:10 [INFO] [stderr] | [INFO] [stderr] 3727 | for (ref_name, intervals) in &distribution { [INFO] [stderr] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_name` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `ref_base` [INFO] [stderr] --> src/main.rs:3996:21 [INFO] [stderr] | [INFO] [stderr] 3996 | let ref_base = if pos < ref_seq.len() as u32 { [INFO] [stderr] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_base` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `header` [INFO] [stderr] --> src/main.rs:4444:9 [INFO] [stderr] | [INFO] [stderr] 4444 | let header = bam.header().to_owned(); [INFO] [stderr] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stderr] [INFO] [stderr] warning: type `PositionData` is more private than the item `ReplicateData::replicates` [INFO] [stderr] --> src/compare.rs:54:5 [INFO] [stderr] | [INFO] [stderr] 54 | pub replicates: Vec, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ field `ReplicateData::replicates` is reachable at visibility `pub(crate)` [INFO] [stderr] | [INFO] [stderr] note: but type `PositionData` is only usable at visibility `pub(self)` [INFO] [stderr] --> src/compare.rs:110:1 [INFO] [stderr] | [INFO] [stderr] 110 | struct PositionData { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] = note: `#[warn(private_interfaces)]` on by default [INFO] [stderr] [INFO] [stderr] warning: field `tid` is never read [INFO] [stderr] --> src/main.rs:398:5 [INFO] [stderr] | [INFO] [stderr] 397 | struct Item { [INFO] [stderr] | ---- field in this struct [INFO] [stderr] 398 | tid: String, [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = note: `Item` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: function `normalize_signal` is never used [INFO] [stderr] --> src/main.rs:1608:4 [INFO] [stderr] | [INFO] [stderr] 1608 | fn normalize_signal( [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: enum `CompareMode` is never used [INFO] [stderr] --> src/compare.rs:12:10 [INFO] [stderr] | [INFO] [stderr] 12 | pub enum CompareMode { [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: field `test_type` is never read [INFO] [stderr] --> src/compare.rs:43:9 [INFO] [stderr] | [INFO] [stderr] 42 | pub struct StatisticalResult { [INFO] [stderr] | ----------------- field in this struct [INFO] [stderr] 43 | pub test_type: StatisticalTest, [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `StatisticalResult` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: struct `ReplicateData` is never constructed [INFO] [stderr] --> src/compare.rs:52:12 [INFO] [stderr] | [INFO] [stderr] 52 | pub struct ReplicateData { [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: struct `ComparisonResult` is never constructed [INFO] [stderr] --> src/compare.rs:59:12 [INFO] [stderr] | [INFO] [stderr] 59 | pub struct ComparisonResult { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: struct `DiffScanResult` is never constructed [INFO] [stderr] --> src/compare.rs:73:12 [INFO] [stderr] | [INFO] [stderr] 73 | pub struct DiffScanResult { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: struct `DeltaSHAPEResult` is never constructed [INFO] [stderr] --> src/compare.rs:89:12 [INFO] [stderr] | [INFO] [stderr] 89 | pub struct DeltaSHAPEResult { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: struct `NormalizationParams` is never constructed [INFO] [stderr] --> src/compare.rs:104:12 [INFO] [stderr] | [INFO] [stderr] 104 | pub struct NormalizationParams { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: fields `ins`, `del`, `a`, `c`, `g`, and `t` are never read [INFO] [stderr] --> src/compare.rs:118:5 [INFO] [stderr] | [INFO] [stderr] 110 | struct PositionData { [INFO] [stderr] | ------------ fields in this struct [INFO] [stderr] ... [INFO] [stderr] 118 | ins: usize, [INFO] [stderr] | ^^^ [INFO] [stderr] 119 | del: usize, [INFO] [stderr] | ^^^ [INFO] [stderr] 120 | a: u32, [INFO] [stderr] | ^ [INFO] [stderr] 121 | c: u32, [INFO] [stderr] | ^ [INFO] [stderr] 122 | g: u32, [INFO] [stderr] | ^ [INFO] [stderr] 123 | t: u32, [INFO] [stderr] | ^ [INFO] [stderr] | [INFO] [stderr] = note: `PositionData` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: function `normalize_reactivity_data` is never used [INFO] [stderr] --> src/compare.rs:437:4 [INFO] [stderr] | [INFO] [stderr] 437 | fn normalize_reactivity_data( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `quantile_normalization` is never used [INFO] [stderr] --> src/compare.rs:451:4 [INFO] [stderr] | [INFO] [stderr] 451 | fn quantile_normalization( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `robust_normalization` is never used [INFO] [stderr] --> src/compare.rs:500:4 [INFO] [stderr] | [INFO] [stderr] 500 | fn robust_normalization( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `median_normalization` is never used [INFO] [stderr] --> src/compare.rs:535:4 [INFO] [stderr] | [INFO] [stderr] 535 | fn median_normalization( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `calculate_mad` is never used [INFO] [stderr] --> src/compare.rs:575:4 [INFO] [stderr] | [INFO] [stderr] 575 | fn calculate_mad(values: &[f64], median: f64) -> f64 { [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `compare_samples` is never used [INFO] [stderr] --> src/compare.rs:1764:8 [INFO] [stderr] | [INFO] [stderr] 1764 | pub fn compare_samples( [INFO] [stderr] | ^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `load_reference_sequence` is never used [INFO] [stderr] --> src/convert.rs:372:4 [INFO] [stderr] | [INFO] [stderr] 372 | fn load_reference_sequence(fasta_path: &str, chr_name: Option<&str>) -> Result, Box> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: constant `MIN_SHARED_FRACTION` is never used [INFO] [stderr] --> src/duet.rs:29:7 [INFO] [stderr] | [INFO] [stderr] 29 | const MIN_SHARED_FRACTION: f64 = 0.15; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: constant `MIN_REACTIVITY_CORRELATION` is never used [INFO] [stderr] --> src/duet.rs:33:7 [INFO] [stderr] | [INFO] [stderr] 33 | const MIN_REACTIVITY_CORRELATION: f64 = 0.60; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `plot_single_track` is never used [INFO] [stderr] --> src/duet.rs:3555:4 [INFO] [stderr] | [INFO] [stderr] 3555 | fn plot_single_track( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: struct `ReactivityData` is never constructed [INFO] [stderr] --> src/norm.rs:97:8 [INFO] [stderr] | [INFO] [stderr] 97 | struct ReactivityData { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `dynamic_window_norm` is never used [INFO] [stderr] --> src/norm.rs:475:4 [INFO] [stderr] | [INFO] [stderr] 475 | fn dynamic_window_norm( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `find_adaptive_window` is never used [INFO] [stderr] --> src/norm.rs:581:4 [INFO] [stderr] | [INFO] [stderr] 581 | fn find_adaptive_window( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `find_dynamic_window` is never used [INFO] [stderr] --> src/norm.rs:620:4 [INFO] [stderr] | [INFO] [stderr] 620 | fn find_dynamic_window( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `normalize_window` is never used [INFO] [stderr] --> src/norm.rs:630:4 [INFO] [stderr] | [INFO] [stderr] 630 | fn normalize_window(values: &[f64], norm_method: &StopNormMethod) -> Vec { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: struct `SvgElement` is never constructed [INFO] [stderr] --> src/plot.rs:75:12 [INFO] [stderr] | [INFO] [stderr] 75 | pub struct SvgElement { [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: field `is_high` is never read [INFO] [stderr] --> src/plot.rs:663:5 [INFO] [stderr] | [INFO] [stderr] 657 | struct GenePlotTask { [INFO] [stderr] | ------------ field in this struct [INFO] [stderr] ... [INFO] [stderr] 663 | is_high: bool, [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `GenePlotTask` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: fields `gene_id` and `cov_x_depth` are never read [INFO] [stderr] --> src/plot.rs:668:5 [INFO] [stderr] | [INFO] [stderr] 667 | struct GeneStat { [INFO] [stderr] | -------- fields in this struct [INFO] [stderr] 668 | gene_id: String, [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 671 | cov_x_depth: f64, [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `GeneStat` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: function `find_best_shift_for_base` is never used [INFO] [stderr] --> src/plot.rs:2155:8 [INFO] [stderr] | [INFO] [stderr] 2155 | pub fn find_best_shift_for_base( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: struct `ProgressBar` is never constructed [INFO] [stderr] --> src/progress.rs:4:12 [INFO] [stderr] | [INFO] [stderr] 4 | pub struct ProgressBar { [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: associated items `new`, `with_width`, `update`, `display`, `finish`, and `with_description` are never used [INFO] [stderr] --> src/progress.rs:13:12 [INFO] [stderr] | [INFO] [stderr] 11 | impl ProgressBar { [INFO] [stderr] | ---------------- associated items in this implementation [INFO] [stderr] 12 | /// Create a new progress bar [INFO] [stderr] 13 | pub fn new(total: usize) -> Self { [INFO] [stderr] | ^^^ [INFO] [stderr] ... [INFO] [stderr] 23 | pub fn with_width(mut self, width: usize) -> Self { [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 29 | pub fn update(&mut self, current: usize) -> io::Result<()> { [INFO] [stderr] | ^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 47 | fn display(&self) -> io::Result<()> { [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 77 | pub fn finish(&mut self) -> io::Result<()> { [INFO] [stderr] | ^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 85 | pub fn with_description(mut self, description: &str) -> io::Result<()> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: struct `DescriptiveProgress` is never constructed [INFO] [stderr] --> src/progress.rs:162:12 [INFO] [stderr] | [INFO] [stderr] 162 | pub struct DescriptiveProgress { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: associated items `new`, `update`, and `finish` are never used [INFO] [stderr] --> src/progress.rs:171:12 [INFO] [stderr] | [INFO] [stderr] 169 | impl DescriptiveProgress { [INFO] [stderr] | ------------------------ associated items in this implementation [INFO] [stderr] 170 | /// Create a new descriptive progress displayer [INFO] [stderr] 171 | pub fn new(total: usize, description: &str) -> Self { [INFO] [stderr] | ^^^ [INFO] [stderr] ... [INFO] [stderr] 181 | pub fn update(&mut self, current: usize) -> io::Result<()> { [INFO] [stderr] | ^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 203 | pub fn finish(&mut self) -> io::Result<()> { [INFO] [stderr] | ^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: fields `vs_low_p50`, `vs_overall_p50`, and `correction_p50` are never read [INFO] [stderr] --> src/reactivity.rs:270:5 [INFO] [stderr] | [INFO] [stderr] 267 | struct DistributionTargets { [INFO] [stderr] | ------------------- fields in this struct [INFO] [stderr] ... [INFO] [stderr] 270 | vs_low_p50: f64, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 277 | vs_overall_p50: f64, [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 284 | correction_p50: f64, [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `calculate_auc_for_k` is never used [INFO] [stderr] --> src/reactivity.rs:713:4 [INFO] [stderr] | [INFO] [stderr] 713 | fn calculate_auc_for_k( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused `Result` that must be used [INFO] [stderr] --> src/main.rs:1442:5 [INFO] [stderr] | [INFO] [stderr] 1442 | bam.set_threads(1); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stderr] = note: `#[warn(unused_must_use)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] help: use `let _ = ...` to ignore the resulting value [INFO] [stderr] | [INFO] [stderr] 1442 | let _ = bam.set_threads(1); [INFO] [stderr] | +++++++ [INFO] [stderr] [INFO] [stderr] warning: unused `Result` that must be used [INFO] [stderr] --> src/main.rs:3493:13 [INFO] [stderr] | [INFO] [stderr] 3493 | bam.set_threads(1); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stderr] help: use `let _ = ...` to ignore the resulting value [INFO] [stderr] | [INFO] [stderr] 3493 | let _ = bam.set_threads(1); [INFO] [stderr] | +++++++ [INFO] [stderr] [INFO] [stderr] warning: unused `Result` that must be used [INFO] [stderr] --> src/main.rs:4442:5 [INFO] [stderr] | [INFO] [stderr] 4442 | bam.set_threads(1); // Avoid internal multi-threading conflicts [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stderr] help: use `let _ = ...` to ignore the resulting value [INFO] [stderr] | [INFO] [stderr] 4442 | let _ = bam.set_threads(1); // Avoid internal multi-threading conflicts [INFO] [stderr] | +++++++ [INFO] [stderr] [INFO] [stderr] warning: unused `Result` that must be used [INFO] [stderr] --> src/main.rs:4475:9 [INFO] [stderr] | [INFO] [stderr] 4475 | window_bam.set_threads(1); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stderr] help: use `let _ = ...` to ignore the resulting value [INFO] [stderr] | [INFO] [stderr] 4475 | let _ = window_bam.set_threads(1); [INFO] [stderr] | +++++++ [INFO] [stderr] [INFO] [stderr] warning: comparison is useless due to type limits [INFO] [stderr] --> src/main.rs:4549:32 [INFO] [stderr] | [INFO] [stderr] 4549 | ... if qpos >= 0 && (qpos as usize) < quals.len() { [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_comparisons)]` on by default [INFO] [stderr] [INFO] [stderr] warning: function `compute_scan_Q` should have a snake case name [INFO] [stderr] --> src/compare.rs:274:4 [INFO] [stderr] | [INFO] [stderr] 274 | fn compute_scan_Q( [INFO] [stderr] | ^^^^^^^^^^^^^^ help: convert the identifier to snake case: `compute_scan_q` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: `modtector` (bin "modtector" test) generated 148 warnings (run `cargo fix --bin "modtector" -p modtector --tests` to apply 64 suggestions) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.24s [INFO] [stderr] Running unittests src/extract_transcripts_main.rs (/opt/rustwide/target/debug/deps/extract_transcripts-9c7e583b23c7ae78) [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/modtector-ba25f1d11c94ef6b) [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "9b0f875c99da72010dbd65b2a40abab1ae13ec0e63398786192b2a3fc052f797", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9b0f875c99da72010dbd65b2a40abab1ae13ec0e63398786192b2a3fc052f797", kill_on_drop: false }` [INFO] [stdout] 9b0f875c99da72010dbd65b2a40abab1ae13ec0e63398786192b2a3fc052f797