[INFO] fetching crate bamnado 0.3.6... [INFO] checking bamnado-0.3.6 against try#51de2e90f91fdec6cf64ff542a4e15b9c177a797 for pr-147294 [INFO] extracting crate bamnado 0.3.6 into /workspace/builds/worker-1-tc2/source [INFO] started tweaking crates.io crate bamnado 0.3.6 [INFO] finished tweaking crates.io crate bamnado 0.3.6 [INFO] tweaked toml for crates.io crate bamnado 0.3.6 written to /workspace/builds/worker-1-tc2/source/Cargo.toml [INFO] validating manifest of crates.io crate bamnado 0.3.6 on toolchain 51de2e90f91fdec6cf64ff542a4e15b9c177a797 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+51de2e90f91fdec6cf64ff542a4e15b9c177a797" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate bamnado 0.3.6 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" "+51de2e90f91fdec6cf64ff542a4e15b9c177a797" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+51de2e90f91fdec6cf64ff542a4e15b9c177a797" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 43a054a1e5677692778a43797eac8760a567556474834c59dec2d71dedda47dc [INFO] running `Command { std: "docker" "start" "-a" "43a054a1e5677692778a43797eac8760a567556474834c59dec2d71dedda47dc", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "43a054a1e5677692778a43797eac8760a567556474834c59dec2d71dedda47dc", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "43a054a1e5677692778a43797eac8760a567556474834c59dec2d71dedda47dc", kill_on_drop: false }` [INFO] [stdout] 43a054a1e5677692778a43797eac8760a567556474834c59dec2d71dedda47dc [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+51de2e90f91fdec6cf64ff542a4e15b9c177a797" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 896611ac079dca106afc3af72812fe434014f49a7be27423d18aaba652d00b5f [INFO] running `Command { std: "docker" "start" "-a" "896611ac079dca106afc3af72812fe434014f49a7be27423d18aaba652d00b5f", kill_on_drop: false }` [INFO] [stderr] Compiling libm v0.2.15 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Checking foldhash v0.1.5 [INFO] [stderr] Checking smallvec v1.15.1 [INFO] [stderr] Checking num_cpus v1.17.0 [INFO] [stderr] Compiling futures-macro v0.3.31 [INFO] [stderr] Checking serde v1.0.219 [INFO] [stderr] Checking rayon-core v1.12.1 [INFO] [stderr] Compiling ring v0.17.14 [INFO] [stderr] Checking miniz_oxide v0.8.9 [INFO] [stderr] Checking crc32fast v1.4.2 [INFO] [stderr] Checking tracing v0.1.41 [INFO] [stderr] Compiling bytemuck_derive v1.9.3 [INFO] [stderr] Compiling rustls v0.23.29 [INFO] [stderr] Compiling rustversion v1.0.21 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Checking icu_normalizer v2.0.0 [INFO] [stderr] Checking parking_lot_core v0.9.11 [INFO] [stderr] Compiling rand_core v0.6.4 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Compiling regex-syntax v0.8.5 [INFO] [stderr] Compiling serde_json v1.0.140 [INFO] [stderr] Compiling psm v0.1.26 [INFO] [stderr] Compiling stacker v0.1.21 [INFO] [stderr] Checking parking_lot v0.12.4 [INFO] [stderr] Compiling zstd-sys v2.0.15+zstd.1.5.7 [INFO] [stderr] Compiling signal-hook v0.3.18 [INFO] [stderr] Checking array-init-cursor v0.2.1 [INFO] [stderr] Checking rayon v1.10.0 [INFO] [stderr] Checking flate2 v1.1.2 [INFO] [stderr] Checking idna_adapter v1.2.1 [INFO] [stderr] Checking rand v0.9.1 [INFO] [stderr] Compiling slotmap v1.0.7 [INFO] [stderr] Checking idna v1.0.3 [INFO] [stderr] Checking futures-util v0.3.31 [INFO] [stderr] Compiling lz4-sys v1.11.1+lz4-1.10.0 [INFO] [stderr] Compiling polars-utils v0.49.1 [INFO] [stderr] Checking url v2.5.4 [INFO] [stderr] Checking castaway v0.2.3 [INFO] [stderr] Compiling phf_generator v0.11.3 [INFO] [stderr] Checking simdutf8 v0.1.5 [INFO] [stderr] Compiling zstd-safe v7.2.4 [INFO] [stderr] Compiling phf_codegen v0.11.3 [INFO] [stderr] Checking phf_shared v0.11.3 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Checking memmap2 v0.9.5 [INFO] [stderr] Compiling polars-schema v0.49.1 [INFO] [stderr] Checking phf v0.11.3 [INFO] [stderr] Compiling polars-arrow v0.49.1 [INFO] [stderr] Checking crossbeam-channel v0.5.15 [INFO] [stderr] Compiling polars-compute v0.49.1 [INFO] [stderr] Checking dyn-clone v1.0.19 [INFO] [stderr] Checking streaming-iterator v0.1.9 [INFO] [stderr] Checking ethnum v1.5.2 [INFO] [stderr] Checking debug_unsafe v0.1.3 [INFO] [stderr] Checking skiplist v0.5.1 [INFO] [stderr] Compiling ahash v0.8.12 [INFO] [stderr] Checking atoi_simd v0.16.1 [INFO] [stderr] Checking fast-float2 v0.2.3 [INFO] [stderr] Checking unicode-width v0.2.1 [INFO] [stderr] Checking bytemuck v1.23.1 [INFO] [stderr] Compiling polars-core v0.49.1 [INFO] [stderr] Checking uuid v1.17.0 [INFO] [stderr] Checking lexical-util v1.0.6 [INFO] [stderr] Compiling polars-ops v0.49.1 [INFO] [stderr] Checking boxcar v0.2.13 [INFO] [stderr] Checking xxhash-rust v0.8.15 [INFO] [stderr] Compiling blake3 v1.8.2 [INFO] [stderr] Compiling async-stream-impl v0.3.6 [INFO] [stderr] Checking bstr v1.12.0 [INFO] [stderr] Checking fallible-streaming-iterator v0.1.9 [INFO] [stderr] Checking bit-vec v0.8.0 [INFO] [stderr] Compiling regex-automata v0.4.9 [INFO] [stderr] Checking streaming-decompression v0.1.2 [INFO] [stderr] Compiling recursive-proc-macro-impl v0.1.1 [INFO] [stderr] Compiling polars-plan v0.49.1 [INFO] [stderr] Checking async-stream v0.3.6 [INFO] [stderr] Checking noodles-core v0.17.0 [INFO] [stderr] Compiling matrixmultiply v0.3.10 [INFO] [stderr] Checking glob v0.3.2 [INFO] [stderr] Checking home v0.5.11 [INFO] [stderr] Checking recursive v0.1.1 [INFO] [stderr] Checking lexical-parse-integer v1.0.5 [INFO] [stderr] Checking lexical-write-integer v1.0.5 [INFO] [stderr] Checking concurrent-queue v2.5.0 [INFO] [stderr] Checking safe_arch v0.7.4 [INFO] [stderr] Compiling bzip2-sys v0.1.13+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Checking lexical-parse-float v1.0.5 [INFO] [stderr] Checking event-listener v5.4.0 [INFO] [stderr] Checking rmp v0.8.14 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking bytes v1.10.1 [INFO] [stderr] Checking hashbrown v0.15.4 [INFO] [stderr] Checking bitflags v2.9.1 [INFO] [stderr] Checking chrono v0.4.41 [INFO] [stderr] Checking serde_urlencoded v0.7.1 [INFO] [stderr] Checking quick-xml v0.37.5 [INFO] [stderr] Checking bincode v1.3.3 [INFO] [stderr] Checking rmp-serde v1.3.0 [INFO] [stderr] Checking raw-cpuid v11.5.0 [INFO] [stderr] Checking compact_str v0.8.1 [INFO] [stderr] Checking rustix v0.38.44 [INFO] [stderr] Checking rustix v1.0.7 [INFO] [stderr] Checking tokio v1.46.1 [INFO] [stderr] Checking http v1.3.1 [INFO] [stderr] Checking hashbrown v0.14.5 [INFO] [stderr] Checking indexmap v2.10.0 [INFO] [stderr] Checking planus v1.1.1 [INFO] [stderr] Checking futures-executor v0.3.31 [INFO] [stderr] Checking argminmax v0.6.3 [INFO] [stderr] Checking futures v0.3.31 [INFO] [stderr] Checking polars-parquet-format v0.1.0 [INFO] [stderr] Checking lexical-write-float v1.0.5 [INFO] [stderr] Checking now v0.1.3 [INFO] [stderr] Checking num-complex v0.4.6 [INFO] [stderr] Checking crossterm v0.28.1 [INFO] [stderr] Checking http-body v1.0.1 [INFO] [stderr] Checking http-body-util v0.1.3 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Checking comfy-table v7.1.4 [INFO] [stderr] Checking polars-arrow-format v0.2.0 [INFO] [stderr] Checking lexical-core v1.0.5 [INFO] [stderr] Compiling regex v1.11.1 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Checking event-listener-strategy v0.5.4 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Checking wide v0.7.33 [INFO] [stderr] Compiling libdeflate-sys v0.13.0 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Checking crossbeam-queue v0.3.12 [INFO] [stderr] Checking rustls-webpki v0.103.4 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling polars-stream v0.49.1 [INFO] [stderr] Compiling rustls v0.21.12 [INFO] [stderr] Checking sct v0.7.1 [INFO] [stderr] Checking rustls-webpki v0.101.7 [INFO] [stderr] Compiling parse-zoneinfo v0.3.1 [INFO] [stderr] Checking fs4 v0.13.1 [INFO] [stderr] Checking async-channel v2.5.0 [INFO] [stderr] Checking digest v0.10.7 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking num-rational v0.4.2 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling polars-lazy v0.49.1 [INFO] [stderr] Compiling portable-atomic v1.11.1 [INFO] [stderr] Checking xz2 v0.1.7 [INFO] [stderr] Checking md-5 v0.10.6 [INFO] [stderr] Compiling chrono-tz-build v0.4.1 [INFO] [stderr] Checking bzip2 v0.5.2 [INFO] [stderr] Checking ndarray v0.16.1 [INFO] [stderr] Checking webpki v0.22.4 [INFO] [stderr] Checking http v0.2.12 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Checking env_filter v0.1.3 [INFO] [stderr] Compiling chrono-tz v0.10.3 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Checking csv-core v0.1.12 [INFO] [stderr] Checking thiserror v1.0.69 [INFO] [stderr] Compiling polars v0.49.1 [INFO] [stderr] Checking ufmt-write v0.1.0 [INFO] [stderr] Checking fixedbitset v0.5.7 [INFO] [stderr] Checking jiff v0.2.15 [INFO] [stderr] Checking tempfile v3.20.0 [INFO] [stderr] Checking petgraph v0.8.2 [INFO] [stderr] Checking enum-map v2.7.3 [INFO] [stderr] Checking bio-types v1.0.4 [INFO] [stderr] Checking csv v1.3.1 [INFO] [stderr] Checking alga v0.9.3 [INFO] [stderr] Checking simba v0.9.0 [INFO] [stderr] Checking bv v0.11.1 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking multimap v0.10.1 [INFO] [stderr] Checking tokio-util v0.7.15 [INFO] [stderr] Checking tower v0.5.2 [INFO] [stderr] Checking async-compression v0.4.25 [INFO] [stderr] Checking h2 v0.4.11 [INFO] [stderr] Checking noodles-bgzf v0.41.0 [INFO] [stderr] Checking libdeflater v0.13.0 [INFO] [stderr] Checking noodles-csi v0.49.0 [INFO] [stderr] Checking noodles-fasta v0.54.0 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking ordered-float v5.0.0 [INFO] [stderr] Checking attohttpc v0.25.0 [INFO] [stderr] Checking tokio-rustls v0.26.2 [INFO] [stderr] Checking bit-set v0.8.0 [INFO] [stderr] Checking tower-http v0.6.6 [INFO] [stderr] Checking console v0.15.11 [INFO] [stderr] Checking byteordered v0.6.0 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking noodles-sam v0.77.0 [INFO] [stderr] Checking noodles-tabix v0.55.0 [INFO] [stderr] Checking number_prefix v0.4.0 [INFO] [stderr] Checking editdistancek v1.0.2 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking index_list v0.2.16 [INFO] [stderr] Checking strum v0.26.3 [INFO] [stderr] Checking bytecount v0.6.9 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Checking noodles-bed v0.26.0 [INFO] [stderr] Checking indicatif v0.17.11 [INFO] [stderr] Checking crossbeam v0.8.4 [INFO] [stderr] Checking rust-lapper v1.2.0 [INFO] [stderr] Compiling ufmt-macros v0.3.0 [INFO] [stderr] Checking sprs v0.11.3 [INFO] [stderr] Checking ufmt v0.2.0 [INFO] [stderr] Checking bigtools v0.5.6 [INFO] [stderr] Checking noodles-bam v0.81.0 [INFO] [stderr] Checking hyper v1.6.0 [INFO] [stderr] Checking zstd v0.13.3 [INFO] [stderr] Checking env_logger v0.11.8 [INFO] [stderr] Checking colog v1.3.0 [INFO] [stderr] Checking hyper-util v0.1.15 [INFO] [stderr] Checking noodles-cram v0.84.0 [INFO] [stderr] Checking hyper-rustls v0.27.7 [INFO] [stderr] Checking reqwest v0.12.22 [INFO] [stderr] Checking nalgebra v0.33.2 [INFO] [stderr] Checking object_store v0.12.2 [INFO] [stderr] Checking noodles v0.99.0 [INFO] [stderr] Checking polars-error v0.49.1 [INFO] [stderr] Checking lz4 v1.28.1 [INFO] [stderr] Checking statrs v0.18.0 [INFO] [stderr] Checking bio v2.3.0 [INFO] [stderr] Checking polars-row v0.49.1 [INFO] [stderr] Checking polars-parquet v0.49.1 [INFO] [stderr] Checking polars-time v0.49.1 [INFO] [stderr] Checking polars-io v0.49.1 [INFO] [stderr] Checking polars-expr v0.49.1 [INFO] [stderr] Checking polars-mem-engine v0.49.1 [INFO] [stderr] Checking bamnado v0.3.6 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `warn` [INFO] [stdout] --> src/bam_utils.rs:6:24 [INFO] [stdout] | [INFO] [stdout] 6 | use log::{debug, info, warn}; [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: `noodles::sam::alignment::record::data::field::tag::Tag` [INFO] [stdout] --> src/bam_utils.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use noodles::sam::alignment::record::data::field::tag::Tag; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `BufRead` [INFO] [stdout] --> src/bam_utils.rs:14:15 [INFO] [stdout] | [INFO] [stdout] 14 | use std::io::{BufRead, Write}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `regex::Regex` [INFO] [stdout] --> src/bam_utils.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | use regex::Regex; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashSet` [INFO] [stdout] --> src/spike_in_analysis.rs:1:22 [INFO] [stdout] | [INFO] [stdout] 1 | use ahash::{HashMap, HashSet, HashSetExt}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `error` [INFO] [stdout] --> src/spike_in_analysis.rs:10:11 [INFO] [stdout] | [INFO] [stdout] 10 | use log::{error, info}; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `record::Record` [INFO] [stdout] --> src/spike_in_analysis.rs:11:33 [INFO] [stdout] | [INFO] [stdout] 11 | use noodles::bam::{self as bam, record::Record}; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `alignment::RecordBuf` and `header::Header` [INFO] [stdout] --> src/spike_in_analysis.rs:12:33 [INFO] [stdout] | [INFO] [stdout] 12 | use noodles::sam::{self as sam, alignment::RecordBuf, header::Header}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::ops::Deref` [INFO] [stdout] --> src/coverage_analysis.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::ops::Deref; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `core` [INFO] [stdout] --> src/coverage_analysis.rs:14:20 [INFO] [stdout] | [INFO] [stdout] 14 | use noodles::{bam, core}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `cols`, `mean_horizontal`, and `sum_horizontal` [INFO] [stdout] --> src/coverage_analysis.rs:15:30 [INFO] [stdout] | [INFO] [stdout] 15 | use polars::lazy::dsl::{col, cols, mean_horizontal, sum_horizontal}; [INFO] [stdout] | ^^^^ ^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bigtools::BigWigRead` [INFO] [stdout] --> src/coverage_analysis.rs:21:5 [INFO] [stdout] | [INFO] [stdout] 21 | use bigtools::BigWigRead; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `debug`, `info`, and `warn` [INFO] [stdout] --> src/bam_splitter.rs:6:11 [INFO] [stdout] | [INFO] [stdout] 6 | use log::{debug, info, warn}; [INFO] [stdout] | ^^^^^ ^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `sam` [INFO] [stdout] --> src/bam_splitter.rs:11:20 [INFO] [stdout] | [INFO] [stdout] 11 | use noodles::{bam, sam}; [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Map` and `map::ReferenceSequence` [INFO] [stdout] --> src/bam_splitter.rs:13:43 [INFO] [stdout] | [INFO] [stdout] 13 | use noodles::sam::header::record::value::{map::ReferenceSequence, Map}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::bam_utils::BamStats` [INFO] [stdout] --> src/bam_modifier.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::bam_utils::BamStats; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::genomic_intervals` [INFO] [stdout] --> src/bam_modifier.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use crate::genomic_intervals; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `IntervalMaker` and `Shift` [INFO] [stdout] --> src/bam_modifier.rs:4:32 [INFO] [stdout] | [INFO] [stdout] 4 | use crate::genomic_intervals::{IntervalMaker, Shift}; [INFO] [stdout] | ^^^^^^^^^^^^^ ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crossbeam::channel::unbounded` [INFO] [stdout] --> src/bam_modifier.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use crossbeam::channel::unbounded; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `debug` and `info` [INFO] [stdout] --> src/bam_modifier.rs:10:11 [INFO] [stdout] | [INFO] [stdout] 10 | use log::{debug, info, warn}; [INFO] [stdout] | ^^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Map` and `map::ReferenceSequence` [INFO] [stdout] --> src/bam_modifier.rs:15:43 [INFO] [stdout] | [INFO] [stdout] 15 | use noodles::sam::header::record::value::{Map, map::ReferenceSequence}; [INFO] [stdout] | ^^^ ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `bam` and `sam` [INFO] [stdout] --> src/bam_modifier.rs:16:15 [INFO] [stdout] | [INFO] [stdout] 16 | use noodles::{bam, sam}; [INFO] [stdout] | ^^^ ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `IntoParallelIterator` [INFO] [stdout] --> src/bam_modifier.rs:17:19 [INFO] [stdout] | [INFO] [stdout] 17 | use rayon::iter::{IntoParallelIterator, ParallelIterator}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `warn` [INFO] [stdout] --> src/bam_utils.rs:6:24 [INFO] [stdout] | [INFO] [stdout] 6 | use log::{debug, info, warn}; [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: `noodles::sam::alignment::record::data::field::tag::Tag` [INFO] [stdout] --> src/bam_utils.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use noodles::sam::alignment::record::data::field::tag::Tag; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `BufRead` [INFO] [stdout] --> src/bam_utils.rs:14:15 [INFO] [stdout] | [INFO] [stdout] 14 | use std::io::{BufRead, Write}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `regex::Regex` [INFO] [stdout] --> src/bam_utils.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | use regex::Regex; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashSet` [INFO] [stdout] --> src/spike_in_analysis.rs:1:22 [INFO] [stdout] | [INFO] [stdout] 1 | use ahash::{HashMap, HashSet, HashSetExt}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `error` [INFO] [stdout] --> src/spike_in_analysis.rs:10:11 [INFO] [stdout] | [INFO] [stdout] 10 | use log::{error, info}; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `record::Record` [INFO] [stdout] --> src/spike_in_analysis.rs:11:33 [INFO] [stdout] | [INFO] [stdout] 11 | use noodles::bam::{self as bam, record::Record}; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `alignment::RecordBuf` and `header::Header` [INFO] [stdout] --> src/spike_in_analysis.rs:12:33 [INFO] [stdout] | [INFO] [stdout] 12 | use noodles::sam::{self as sam, alignment::RecordBuf, header::Header}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::ops::Deref` [INFO] [stdout] --> src/coverage_analysis.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::ops::Deref; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `core` [INFO] [stdout] --> src/coverage_analysis.rs:14:20 [INFO] [stdout] | [INFO] [stdout] 14 | use noodles::{bam, core}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `cols`, `mean_horizontal`, and `sum_horizontal` [INFO] [stdout] --> src/coverage_analysis.rs:15:30 [INFO] [stdout] | [INFO] [stdout] 15 | use polars::lazy::dsl::{col, cols, mean_horizontal, sum_horizontal}; [INFO] [stdout] | ^^^^ ^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `debug`, `info`, and `warn` [INFO] [stdout] --> src/bam_splitter.rs:6:11 [INFO] [stdout] | [INFO] [stdout] 6 | use log::{debug, info, warn}; [INFO] [stdout] | ^^^^^ ^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `sam` [INFO] [stdout] --> src/bam_splitter.rs:11:20 [INFO] [stdout] | [INFO] [stdout] 11 | use noodles::{bam, sam}; [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Map` and `map::ReferenceSequence` [INFO] [stdout] --> src/bam_splitter.rs:13:43 [INFO] [stdout] | [INFO] [stdout] 13 | use noodles::sam::header::record::value::{map::ReferenceSequence, Map}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::bam_utils::BamStats` [INFO] [stdout] --> src/bam_modifier.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::bam_utils::BamStats; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::genomic_intervals` [INFO] [stdout] --> src/bam_modifier.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use crate::genomic_intervals; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `IntervalMaker` and `Shift` [INFO] [stdout] --> src/bam_modifier.rs:4:32 [INFO] [stdout] | [INFO] [stdout] 4 | use crate::genomic_intervals::{IntervalMaker, Shift}; [INFO] [stdout] | ^^^^^^^^^^^^^ ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crossbeam::channel::unbounded` [INFO] [stdout] --> src/bam_modifier.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use crossbeam::channel::unbounded; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `debug` and `info` [INFO] [stdout] --> src/bam_modifier.rs:10:11 [INFO] [stdout] | [INFO] [stdout] 10 | use log::{debug, info, warn}; [INFO] [stdout] | ^^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Map` and `map::ReferenceSequence` [INFO] [stdout] --> src/bam_modifier.rs:15:43 [INFO] [stdout] | [INFO] [stdout] 15 | use noodles::sam::header::record::value::{Map, map::ReferenceSequence}; [INFO] [stdout] | ^^^ ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `bam` and `sam` [INFO] [stdout] --> src/bam_modifier.rs:16:15 [INFO] [stdout] | [INFO] [stdout] 16 | use noodles::{bam, sam}; [INFO] [stdout] | ^^^ ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `IntoParallelIterator` [INFO] [stdout] --> src/bam_modifier.rs:17:19 [INFO] [stdout] | [INFO] [stdout] 17 | use rayon::iter::{IntoParallelIterator, ParallelIterator}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> src/bam_splitter.rs:45:17 [INFO] [stdout] | [INFO] [stdout] 45 | Err(e) => { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> src/bam_modifier.rs:49:17 [INFO] [stdout] | [INFO] [stdout] 49 | Err(e) => get_bam_header(&filepath)?, [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> src/bam_splitter.rs:45:17 [INFO] [stdout] | [INFO] [stdout] 45 | Err(e) => { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> src/bam_modifier.rs:49:17 [INFO] [stdout] | [INFO] [stdout] 49 | Err(e) => get_bam_header(&filepath)?, [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Write` [INFO] [stdout] --> src/bam_utils.rs:14:24 [INFO] [stdout] | [INFO] [stdout] 14 | use std::io::{BufRead, Write}; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio_types::annot::loc::Loc` [INFO] [stdout] --> src/bam_utils.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use bio_types::annot::loc::Loc; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ParallelIterator` [INFO] [stdout] --> src/bam_modifier.rs:17:41 [INFO] [stdout] | [INFO] [stdout] 17 | use rayon::iter::{IntoParallelIterator, ParallelIterator}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashSetExt` [INFO] [stdout] --> src/spike_in_analysis.rs:1:31 [INFO] [stdout] | [INFO] [stdout] 1 | use ahash::{HashMap, HashSet, HashSetExt}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `i` [INFO] [stdout] --> src/bam_utils.rs:153:14 [INFO] [stdout] | [INFO] [stdout] 153 | for (i, column) in df.iter().enumerate() { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_i` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bam_utils.rs:528:9 [INFO] [stdout] | [INFO] [stdout] 528 | let mut buf_reader = std::io::BufReader::new(reader); [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 import: `Write` [INFO] [stdout] --> src/bam_utils.rs:14:24 [INFO] [stdout] | [INFO] [stdout] 14 | use std::io::{BufRead, Write}; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio_types::annot::loc::Loc` [INFO] [stdout] --> src/bam_utils.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use bio_types::annot::loc::Loc; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ParallelIterator` [INFO] [stdout] --> src/bam_modifier.rs:17:41 [INFO] [stdout] | [INFO] [stdout] 17 | use rayon::iter::{IntoParallelIterator, ParallelIterator}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashSetExt` [INFO] [stdout] --> src/spike_in_analysis.rs:1:31 [INFO] [stdout] | [INFO] [stdout] 1 | use ahash::{HashMap, HashSet, HashSetExt}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `i` [INFO] [stdout] --> src/bam_utils.rs:153:14 [INFO] [stdout] | [INFO] [stdout] 153 | for (i, column) in df.iter().enumerate() { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_i` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bam_utils.rs:528:9 [INFO] [stdout] | [INFO] [stdout] 528 | let mut buf_reader = std::io::BufReader::new(reader); [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: variable does not need to be mutable [INFO] [stdout] --> src/coverage_analysis.rs:29:19 [INFO] [stdout] | [INFO] [stdout] 29 | fn write_bedgraph(mut df: DataFrame, outfile: PathBuf, ignore_scaffold_chromosomes: bool) -> Result<()> { [INFO] [stdout] | ----^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `chromsizes_refid` [INFO] [stdout] --> src/bam_splitter.rs:106:13 [INFO] [stdout] | [INFO] [stdout] 106 | let chromsizes_refid = bam_stats [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_chromsizes_refid` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `n_total_chunks` [INFO] [stdout] --> src/bam_splitter.rs:111:13 [INFO] [stdout] | [INFO] [stdout] 111 | let n_total_chunks = genomic_chunks.len(); [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_n_total_chunks` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bam_splitter.rs:121:17 [INFO] [stdout] | [INFO] [stdout] 121 | let reader = bam::io::indexed_reader::Builder::default() [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/coverage_analysis.rs:29:19 [INFO] [stdout] | [INFO] [stdout] 29 | fn write_bedgraph(mut df: DataFrame, outfile: PathBuf, ignore_scaffold_chromosomes: bool) -> Result<()> { [INFO] [stdout] | ----^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `chrom` is never read [INFO] [stdout] --> src/bam_utils.rs:170:5 [INFO] [stdout] | [INFO] [stdout] 169 | struct ChromosomeStats { [INFO] [stdout] | --------------- field in this struct [INFO] [stdout] 170 | chrom: String, [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `ChromosomeStats` has a derived impl for the trait `Debug`, but this is 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: fields `file_path` and `contigs` are never read [INFO] [stdout] --> src/bam_utils.rs:232:5 [INFO] [stdout] | [INFO] [stdout] 228 | pub struct BamStats { [INFO] [stdout] | -------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 232 | file_path: PathBuf, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 238 | contigs: Vec>, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `input_header` is never read [INFO] [stdout] --> src/spike_in_analysis.rs:107:5 [INFO] [stdout] | [INFO] [stdout] 104 | pub struct BamSplitter { [INFO] [stdout] | ----------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 107 | input_header: sam::Header, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `convert_bedgraph_to_bigwig` is never used [INFO] [stdout] --> src/coverage_analysis.rs:110:4 [INFO] [stdout] | [INFO] [stdout] 110 | fn convert_bedgraph_to_bigwig( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `chromsizes_refid` [INFO] [stdout] --> src/bam_splitter.rs:106:13 [INFO] [stdout] | [INFO] [stdout] 106 | let chromsizes_refid = bam_stats [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_chromsizes_refid` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `n_total_chunks` [INFO] [stdout] --> src/bam_splitter.rs:111:13 [INFO] [stdout] | [INFO] [stdout] 111 | let n_total_chunks = genomic_chunks.len(); [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_n_total_chunks` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bam_splitter.rs:121:17 [INFO] [stdout] | [INFO] [stdout] 121 | let reader = bam::io::indexed_reader::Builder::default() [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `chrom` is never read [INFO] [stdout] --> src/bam_utils.rs:170:5 [INFO] [stdout] | [INFO] [stdout] 169 | struct ChromosomeStats { [INFO] [stdout] | --------------- field in this struct [INFO] [stdout] 170 | chrom: String, [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `ChromosomeStats` has a derived impl for the trait `Debug`, but this is 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: fields `file_path` and `contigs` are never read [INFO] [stdout] --> src/bam_utils.rs:232:5 [INFO] [stdout] | [INFO] [stdout] 228 | pub struct BamStats { [INFO] [stdout] | -------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 232 | file_path: PathBuf, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 238 | contigs: Vec>, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `input_header` is never read [INFO] [stdout] --> src/spike_in_analysis.rs:107:5 [INFO] [stdout] | [INFO] [stdout] 104 | pub struct BamSplitter { [INFO] [stdout] | ----------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 107 | input_header: sam::Header, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `error` [INFO] [stdout] --> src/main.rs:3:11 [INFO] [stdout] | [INFO] [stdout] 3 | use log::{error, info}; [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: `error` [INFO] [stdout] --> src/main.rs:3:11 [INFO] [stdout] | [INFO] [stdout] 3 | use log::{error, info}; [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::str::FromStr` [INFO] [stdout] --> src/main.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use std::str::FromStr; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::str::FromStr` [INFO] [stdout] --> src/main.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use std::str::FromStr; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `blacklist` [INFO] [stdout] --> src/main.rs:278:15 [INFO] [stdout] | [INFO] [stdout] 278 | (Some(blacklist), None) => { [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_blacklist` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `allow_unknown_mapq` [INFO] [stdout] --> src/main.rs:503:13 [INFO] [stdout] | [INFO] [stdout] 503 | allow_unknown_mapq, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ help: try ignoring the field: `allow_unknown_mapq: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `filter` [INFO] [stdout] --> src/main.rs:510:17 [INFO] [stdout] | [INFO] [stdout] 510 | let filter = create_filter_from_options(filter_options, None)?; [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_filter` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `check_bedgraph_to_bigwig_tool` is never used [INFO] [stdout] --> src/main.rs:310:4 [INFO] [stdout] | [INFO] [stdout] 310 | fn check_bedgraph_to_bigwig_tool() -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `blacklist` [INFO] [stdout] --> src/main.rs:278:15 [INFO] [stdout] | [INFO] [stdout] 278 | (Some(blacklist), None) => { [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_blacklist` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `allow_unknown_mapq` [INFO] [stdout] --> src/main.rs:503:13 [INFO] [stdout] | [INFO] [stdout] 503 | allow_unknown_mapq, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ help: try ignoring the field: `allow_unknown_mapq: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `filter` [INFO] [stdout] --> src/main.rs:510:17 [INFO] [stdout] | [INFO] [stdout] 510 | let filter = create_filter_from_options(filter_options, None)?; [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_filter` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `check_bedgraph_to_bigwig_tool` is never used [INFO] [stdout] --> src/main.rs:310:4 [INFO] [stdout] | [INFO] [stdout] 310 | fn check_bedgraph_to_bigwig_tool() -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 2m 09s [INFO] running `Command { std: "docker" "inspect" "896611ac079dca106afc3af72812fe434014f49a7be27423d18aaba652d00b5f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "896611ac079dca106afc3af72812fe434014f49a7be27423d18aaba652d00b5f", kill_on_drop: false }` [INFO] [stdout] 896611ac079dca106afc3af72812fe434014f49a7be27423d18aaba652d00b5f